mia-2davgmasked

--- /tmp/mia-2.4.7-78ehlp11x/debian/mia-tools-doc_2.4.7-7_all.deb +++ mia-tools-doc_2.4.7-7_all.deb ├── file list │ @@ -1,3 +1,3 @@ │ -rw-r--r-- 0 0 0 4 2021-01-11 21:49:29.000000 debian-binary │ --rw-r--r-- 0 0 0 5932 2021-01-11 21:49:29.000000 control.tar.xz │ --rw-r--r-- 0 0 0 92892 2021-01-11 21:49:29.000000 data.tar.xz │ +-rw-r--r-- 0 0 0 5928 2021-01-11 21:49:29.000000 control.tar.xz │ +-rw-r--r-- 0 0 0 92880 2021-01-11 21:49:29.000000 data.tar.xz ├── control.tar.xz │ ├── control.tar │ │ ├── ./md5sums │ │ │ ├── ./md5sums │ │ │ │┄ Files differ ├── data.tar.xz │ ├── data.tar │ │ ├── ./usr/share/doc/mia-2.4/userref/SecPlugintype2dimagefilter.html │ │ │ @@ -57,15 +57,15 @@ │ │ │

│ │ │

bandpass

intensity bandpass filter. Supported parameters are:

Name	Type	Default	Description
max	float	3.40282e+38	maximum of the band
min	float	0	minimum of the band

│ │ │

binarize

image binarize filter. Supported parameters are:

Name	Type	Default	Description
max	float	3.40282e+38	maximum of accepted range
min	float	0	minimum of accepted range

│ │ │

close

morphological close. Supported parameters are:

Name	Type	Default	Description
hint	set	black	a hint at the main image content Supported values are:(black, white, )
shape	factory	[sphere:r=2]	structuring element. For supported plug-ins see Plugin type: 2dimage/shape

│ │ │

│ │ │ -

combiner

Combine two images with the given combiner operator. if 'reverse' is set to false, the first operator is the image passed through the filter pipeline, and the second image is loaded from the file given with the 'image' parameter the moment the filter is run.. Supported parameters are:

Name	Type	Default	Description
image	io	(required,input)	second image that is needed in the combiner. For supported file types see Plugin type: 2dimage/io
op	factory	(required)	Image combiner to be applied to the images. For supported plug-ins see Plugin type: 2dimage/combiner
reverse	bool	0	reverse the order in which the images passed to the combiner

│ │ │ +

combiner

Name	Type	Default	Description
image	io	(input,required)	second image that is needed in the combiner. For supported file types see Plugin type: 2dimage/io
op	factory	(required)	Image combiner to be applied to the images. For supported plug-ins see Plugin type: 2dimage/combiner
reverse	bool	0	reverse the order in which the images passed to the combiner

│ │ │

convert

image pixel format conversion filter. Supported parameters are:

Name

Type

Default

Description

float

linear conversion parameter a

float

linear conversion parameter b

map

dict

opt

conversion mapping
copy:	copy data when converting
linear:	apply linear transformation x -> a*x+b
range:	apply linear transformation that maps the input data type range to the output data type range
opt:	apply a linear transformation that maps the real input range to the full output range
optstat:	apply a linear transform that maps based on input mean and variation to the full output range

repn

dict

ubyte

output pixel type
bit:	binary data
sbyte:	signed 8 bit
ubyte:	unsigned 8 bit
sshort:	signed 16 bit
ushort:	unsigned 16 bit
sint:	signed 32 bit
uint:	unsigned 32 bit
slong:	signed 64 bit
ulong:	unsigned 64 bit
float:	floating point 32 bit
double:	floating point 64 bit
none:	no pixel type defined

│ │ │

crop

Crop a region of an image, the region is always clamped to the original image size.. Supported parameters are:

Name	Type	Default	Description
end	streamable	[[-1,-1]]	end of crop region
start	streamable	[[0,0]]	start of crop region

│ │ │

dilate

2d image stack dilate filter. Supported parameters are:

Name	Type	Default	Description
hint	set	black	a hint at the main image content Supported values are:(black, white, )
shape	factory	[sphere:r=2]	structuring element. For supported plug-ins see Plugin type: 2dimage/shape

│ │ │

│ │ │ @@ -81,43 +81,43 @@ │ │ │

│ │ │

invert

intensity invert filter. (This plug-in doesn't take parameters)

│ │ │

kmeans

2D image k-means filter. In the output image the pixel value represents the class membership and the class centers are stored as attribute in the image.. Supported parameters are:

Name	Type	Default	Description
c	int in [2, inf)	3	number of classes

│ │ │

label

Label connected components in a binary 2D image.. Supported parameters are:

Name	Type	Default	Description
n	factory	4n	Neighborhood mask to describe connectivity.. For supported plug-ins see Plugin type: 2dimage/shape

│ │ │

│ │ │ -

labelmap

Image filter to remap label id's. Only applicable to images with integer valued intensities/labels.. Supported parameters are:

Name	Type	Default	Description
map	string	(required,input)	Label mapping file

│ │ │ +

labelmap

Image filter to remap label id's. Only applicable to images with integer valued intensities/labels.. Supported parameters are:

Name	Type	Default	Description
map	string	(input,required)	Label mapping file

│ │ │

labelscale

A filter that only creates output voxels that are already created in the input image. Scaling is done by using a voting algorithms that selects the target pixel value based on the highest pixel count of a certain label in the corresponding source region. If the region comprises two labels with the same count, the one with the lower number wins.. Supported parameters are:

Name	Type	Default	Description
out-size	2dbounds	(required)	target size given as two coma separated values

│ │ │

│ │ │ -

load

Load the input image from a file and use it to replace the current image in the pipeline.. Supported parameters are:

Name	Type	Default	Description
file	io	(required,input)	name of the input file to load from.. For supported file types see Plugin type: 2dimage/io

│ │ │ +

load

Load the input image from a file and use it to replace the current image in the pipeline.. Supported parameters are:

Name	Type	Default	Description
file	io	(input,required)	name of the input file to load from.. For supported file types see Plugin type: 2dimage/io

│ │ │

│ │ │ -

mask

2D masking, one of the two input images must by of type bit.. Supported parameters are:

Name

Type

Default

Description

fill

dict

min

fill style for pixels outside of the mask
min:	set values outside the mask to the minimum value found in the image.
zero:	set the values outside the mask to zero.
max:	set values outside the mask to the maximum value found in the image..

input

(required,input)

second input image file name. For supported file types see Plugin type: 2dimage/io

inverse

bool

set to true to use the inverse of the mask for masking

│ │ │ +

mask

2D masking, one of the two input images must by of type bit.. Supported parameters are:

Name

Type

Default

Description

fill

dict

min

fill style for pixels outside of the mask
min:	set values outside the mask to the minimum value found in the image.
zero:	set the values outside the mask to zero.
max:	set values outside the mask to the maximum value found in the image..

input

(input,required)

second input image file name. For supported file types see Plugin type: 2dimage/io

inverse

bool

set to true to use the inverse of the mask for masking

│ │ │

│ │ │ -

maxflow

This filter implements the uses the max-flow min-cut algorithmfor image segmentation. Supported parameters are:

Name	Type	Default	Description
sink-flow	io	(required,input)	Image of float type to define the per-pixel flow to the sink. For supported file types see Plugin type: 2dimage/io
source-flow	io	(required,input)	Image of float type to define the per-pixel flow to the source. For supported file types see Plugin type: 2dimage/io

│ │ │ +

maxflow

This filter implements the uses the max-flow min-cut algorithmfor image segmentation. Supported parameters are:

Name	Type	Default	Description
sink-flow	io	(input,required)	Image of float type to define the per-pixel flow to the sink. For supported file types see Plugin type: 2dimage/io
source-flow	io	(input,required)	Image of float type to define the per-pixel flow to the source. For supported file types see Plugin type: 2dimage/io

│ │ │

mean

2D image mean filter. Supported parameters are:

Name	Type	Default	Description
w	int in [1, inf)	1	half filter width

│ │ │

│ │ │ -

meanvar

Filter that evaluates simultaniously the pixel wise mean and the variance of an image in a given window. Pixel intensities below the given threshold will be ignored and at their loctions the output mean and variation are set to zero. The mean intensity image is directly passed as float image to the pipeline, the variation image is saved to a file given with the varfile parameter.. Supported parameters are:

Name	Type	Default	Description
thresh	double in [0, inf)	0	Intensity thresholding parameter: Pixels with intensities below this threshold will be set to zero, and also not used when evaluating mean and variation
varfile	io	(required,output)	name of the output file to save the variation image too.. For supported file types see Plugin type: 2dimage/io
w	uint in [1, inf)	1	filter width parameter

│ │ │ +

meanvar

Name	Type	Default	Description
thresh	double in [0, inf)	0	Intensity thresholding parameter: Pixels with intensities below this threshold will be set to zero, and also not used when evaluating mean and variation
varfile	io	(output,required)	name of the output file to save the variation image too.. For supported file types see Plugin type: 2dimage/io
w	uint in [1, inf)	1	filter width parameter

│ │ │

median

2D image median filter. Supported parameters are:

Name	Type	Default	Description
w	int in [1, inf)	1	half filter width

│ │ │

│ │ │ -

medianmad

Filter that evaluates simultaniously the pixel wise median and the median absolute deviation (MAD) of an image in a given window. Pixel intensities below the given threshold will be ignored and at their loctions the output median and MAD are set to zero. The median intensity image is directly passed to the pipeline, the variation image is saved to a file given with the varfile parameter. Both output images have the same pixel type like the input image.. Supported parameters are:

Name	Type	Default	Description
madfile	io	(required,output)	name of the output file to save the median absolute deviation image too.. For supported file types see Plugin type: 2dimage/io
thresh	double in [0, inf)	0	Intensity thresholding parameter: Pixels with intensities below this threshold will be set to zero, and also not used when evaluating mean and variation
w	uint in [1, inf)	1	filter width parameter

│ │ │ +

medianmad

Name	Type	Default	Description
madfile	io	(output,required)	name of the output file to save the median absolute deviation image too.. For supported file types see Plugin type: 2dimage/io
thresh	double in [0, inf)	0	Intensity thresholding parameter: Pixels with intensities below this threshold will be set to zero, and also not used when evaluating mean and variation
w	uint in [1, inf)	1	filter width parameter

│ │ │

mlv

Mean of Least Variance 2D image filter. Supported parameters are:

Name	Type	Default	Description
w	int in [1, inf)	1	filter width parameter

│ │ │

ngfnorm

2D image to normalized-gradiend-field-norm filter. (This plug-in doesn't take parameters)

│ │ │

noise

2D image noise filter: add additive or modulated noise to an image. Supported parameters are:

Name	Type	Default	Description
g	factory	[gauss:mu=0,sigma=10]	noise generator. For supported plug-ins see Plugin type: generator/noise
mod	bool	0	additive or modulated noise

│ │ │

open

morphological open. Supported parameters are:

Name	Type	Default	Description
hint	set	black	a hint at the main image content Supported values are:(black, white, )
shape	factory	[sphere:r=2]	structuring element. For supported plug-ins see Plugin type: 2dimage/shape

│ │ │

pruning

Morphological pruning. Pruning until convergence will erase all pixels but closed loops.. Supported parameters are:

Name	Type	Default	Description
iter	int in [1, 1000000]	0	Number of iterations to run, 0=until convergence

│ │ │

│ │ │ -

regiongrow

Region growing startin from a seed until only along increasing gradients. Supported parameters are:

Name	Type	Default	Description
n	factory	8n	Neighborhood shape. For supported plug-ins see Plugin type: 2dimage/shape
seed	io	(required,input)	seed image (bit valued). For supported file types see Plugin type: 2dimage/io

│ │ │ +

regiongrow

Region growing startin from a seed until only along increasing gradients. Supported parameters are:

Name	Type	Default	Description
n	factory	8n	Neighborhood shape. For supported plug-ins see Plugin type: 2dimage/shape
seed	io	(input,required)	seed image (bit valued). For supported file types see Plugin type: 2dimage/io

│ │ │

sandp

salt and pepper 3d filter. Supported parameters are:

Name	Type	Default	Description
thresh	float in (0, inf)	100	thresh value
w	int in [1, inf)	1	filter width parameter

│ │ │

scale

2D image downscale filter. Supported parameters are:

Name	Type	Default	Description
interp	factory	[bspline:d=3]	interpolation method to be used . For supported plug-ins see Plugin type: 1d/splinekernel
s	2dbounds	[[0,0]]	target size as 2D vector
sx	uint in [0, inf)	0	target size in x direction, 0: use input size
sy	uint in [0, inf)	0	target size in y direction, 0: use input size

│ │ │

selectbig

2D label select biggest component filter. (This plug-in doesn't take parameters)

│ │ │

│ │ │ @@ -125,25 +125,25 @@ │ │ │

│ │ │

shmean

2D image filter that evaluates the mean over a given neighborhood shape. Supported parameters are:

Name	Type	Default	Description
shape	factory	8n	neighborhood shape to evaluate the mean. For supported plug-ins see Plugin type: 2dimage/shape

│ │ │

sobel

The 2D Sobel filter for gradient evaluation. Note that the output pixel type of the filtered image is the same as the input pixel type, so converting the input beforehand to a floating point valued image is recommendable.. Supported parameters are:

Name

Type

Default

Description

dir

dict

Gradient direction
x:	gradient in x-direction
y:	gradient in y-direction

│ │ │

sort-label

This plug-in sorts the labels of a gray-scale image so that the lowest label value corresponts to the lable with themost pixels. The background (0) is not touched. (This plug-in doesn't take parameters)

│ │ │

│ │ │ -

sws

seeded watershead. The algorithm extracts exactly so many reagions as initial labels are given in the seed image.. Supported parameters are:

Name	Type	Default	Description
grad	bool	0	Interpret the input image as gradient.
mark	bool	0	Mark the segmented watersheds with a special gray scale value
n	factory	[sphere:r=1]	Neighborhood for watershead region growing. For supported plug-ins see Plugin type: 2dimage/shape
seed	string	(required,input)	seed input image containing the lables for the initial regions

│ │ │ +

sws

seeded watershead. The algorithm extracts exactly so many reagions as initial labels are given in the seed image.. Supported parameters are:

Name	Type	Default	Description
grad	bool	0	Interpret the input image as gradient.
mark	bool	0	Mark the segmented watersheds with a special gray scale value
n	factory	[sphere:r=1]	Neighborhood for watershead region growing. For supported plug-ins see Plugin type: 2dimage/shape
seed	string	(input,required)	seed input image containing the lables for the initial regions

│ │ │

│ │ │ -

tee

Save the input image to a file and also pass it through to the next filter. Supported parameters are:

Name	Type	Default	Description
file	io	(required,output)	name of the output file to save the image too.. For supported file types see Plugin type: 2dimage/io

│ │ │ +

tee

Save the input image to a file and also pass it through to the next filter. Supported parameters are:

Name	Type	Default	Description
file	io	(output,required)	name of the output file to save the image too.. For supported file types see Plugin type: 2dimage/io

│ │ │

thinning

Morphological thinning. Thinning until convergence will result in a 8-connected skeleton. Supported parameters are:

Name	Type	Default	Description
iter	int in [1, 1000000]	0	Number of iterations to run, 0=until convergence

│ │ │

thresh

This filter sets all pixels of an image to zero that fall below a certain threshold and whose neighbours in a given neighborhood shape also fall below a this threshold. Supported parameters are:

Name	Type	Default	Description
shape	factory	4n	neighborhood shape to take into account. For supported plug-ins see Plugin type: 2dimage/shape
thresh	double	5	The threshold value

│ │ │

tmean

2D image thresholded tmean filter: The output pixel value is zero if the input pixel value is below the given threshold, otherwise the pixels in the evaluation windows are only considered if the input pixel intensity is above the threshold.. Supported parameters are:

Name	Type	Default	Description
t	float	0	Threshold for pixels not to take into account
w	int in [1, inf)	1	half filter width

│ │ │

│ │ │ -

transform

Transform the input image with the given transformation.. Supported parameters are:

Name	Type	Default	Description
file	io	(required,input)	Name of the file containing the transformation.. For supported file types see Plugin type: 2dtransform/io

│ │ │ +

transform

Transform the input image with the given transformation.. Supported parameters are:

Name	Type	Default	Description
file	io	(input,required)	Name of the file containing the transformation.. For supported file types see Plugin type: 2dtransform/io

│ │ │

ws

basic watershead segmentation.. Supported parameters are:

Name	Type	Default	Description
evalgrad	bool	0	Set to 1 if the input image does not represent a gradient norm image
mark	bool	0	Mark the segmented watersheds with a special gray scale value
n	factory	[sphere:r=1]	Neighborhood for watershead region growing. For supported plug-ins see Plugin type: 2dimage/shape
thresh	float in [0, 1)	0	Relative gradient norm threshold. The actual value threshold value is thresh * (max_grad - min_grad) + min_grad. Bassins separated by gradients with a lower norm will be joined

│ │ │

Plugin consumers:

│ │ │ mia-2dimagefilter │ │ │ mia-2dimagefilterstack │ │ │ mia-2dsegment-fuzzyw │ │ │ mia-2dseries2dordermedian │ │ ├── ./usr/share/doc/mia-2.4/userref/SecPlugintype2dstackfilter.html │ │ │ @@ -16,19 +16,19 @@ │ │ │

│ │ │

dilate

2D Stack morphological filter 'dilate'. Supported parameters are:

Name	Type	Default	Description
shape	factory	6n	structuring element. For supported plug-ins see Plugin type: 3dimage/shape

│ │ │

erode

2D Stack morphological filter 'erode'. Supported parameters are:

Name	Type	Default	Description
shape	factory	6n	structuring element. For supported plug-ins see Plugin type: 3dimage/shape

│ │ │

gauss

Gauss 2D fifo filter. Supported parameters are:

Name	Type	Default	Description
w	int in [1, inf)	1	filter width parameter (2*w+1)

│ │ │

│ │ │ -

label

Stack Label filter. Supported parameters are:

Name	Type	Default	Description
map	string	(required,input)	Mapfile to save label numbers that are joined
n	factory	4n	2D neighbourhood shape to define connectedness. For supported plug-ins see Plugin type: 2dimage/shape

│ │ │ +

label

Stack Label filter. Supported parameters are:

Name	Type	Default	Description
map	string	(input,required)	Mapfile to save label numbers that are joined
n	factory	4n	2D neighbourhood shape to define connectedness. For supported plug-ins see Plugin type: 2dimage/shape

│ │ │

median

median 2D fifo filter. Supported parameters are:

Name	Type	Default	Description
w	int in [1, inf)	1	filter width parameter

│ │ │

mlv

Mean of Least Variance 2D stack image filter. Supported parameters are:

Name	Type	Default	Description
w	int in [1, inf)	1	filter width parameter

│ │ │

open

2D Stack morphological filter 'open'. Supported parameters are:

Name	Type	Default	Description
shape	factory	6n	structuring element. For supported plug-ins see Plugin type: 3dimage/shape

│ │ │

│ │ │ -

regiongrow

Run a region-growing filter on a stack of images that comprise a 3D image. The region growing is based on class probabilities obtained from a c-means classification of the pixel intensities. One seed thresh is use to initiate a region, and another (lower) threshold is used to stop the region growing. By holding a number of 3D slices in the working memory to permit the region to grow "backwards " in the stack a Quasi-3D processing is achieved. However, with complex structures the region growing may not properly be segmented.. Supported parameters are:

Name	Type	Default	Description
class	int in [0, inf)	2	class to be segmented
depth	int in [1, inf)	10	number of slices to keep during processing
low	float in (0, 1]	0.5	low threshold for acceptance probability
map	string	(required,input)	seed class map
seed	float in (0, 1]	0.98	threshold for seed probability

│ │ │ +

regiongrow

Name	Type	Default	Description
class	int in [0, inf)	2	class to be segmented
depth	int in [1, inf)	10	number of slices to keep during processing
low	float in (0, 1]	0.5	low threshold for acceptance probability
map	string	(input,required)	seed class map
seed	float in (0, 1]	0.98	threshold for seed probability

│ │ │

Plugin consumers:

│ │ │ mia-2dstackfilter │ │ │

Prev	Up	Next
Plugin type: 2dimage/transform	Home	Plugin type: 2dtransform/io

│ │ ├── ./usr/share/doc/mia-2.4/userref/SecPlugintype3dimagefilter.html │ │ │ @@ -45,15 +45,15 @@ │ │ │

│ │ │

bandpass

intensity bandpass filter. Supported parameters are:

Name	Type	Default	Description
max	float	3.40282e+38	maximum of the band
min	float	0	minimum of the band

│ │ │

binarize

image binarize filter. Supported parameters are:

Name	Type	Default	Description
max	float	3.40282e+38	maximum of accepted range
min	float	0	minimum of accepted range

│ │ │

close

morphological close. Supported parameters are:

Name	Type	Default	Description
hint	string	black	a hint at the main image content (black\|white)
shape	factory	[sphere:r=2]	structuring element. For supported plug-ins see Plugin type: 3dimage/shape

│ │ │

│ │ │ -

combiner

Name	Type	Default	Description
image	io	(required,input)	second image that is needed in the combiner. For supported file types see Plugin type: 3dimage/io
op	factory	(required)	Image combiner to be applied to the images. For supported plug-ins see Plugin type: 3dimage/combiner
reverse	bool	0	reverse the order in which the images passed to the combiner

│ │ │ +

combiner

Name	Type	Default	Description
image	io	(input,required)	second image that is needed in the combiner. For supported file types see Plugin type: 3dimage/io
op	factory	(required)	Image combiner to be applied to the images. For supported plug-ins see Plugin type: 3dimage/combiner
reverse	bool	0	reverse the order in which the images passed to the combiner

│ │ │

convert

image pixel format conversion filter. Supported parameters are:

Name

Type

Default

Description

float

linear conversion parameter a

float

linear conversion parameter b

map

dict

opt

conversion mapping
copy:	copy data when converting
linear:	apply linear transformation x -> a*x+b
range:	apply linear transformation that maps the input data type range to the output data type range
opt:	apply a linear transformation that maps the real input range to the full output range
optstat:	apply a linear transform that maps based on input mean and variation to the full output range

repn

dict

ubyte

output pixel type
bit:	binary data
sbyte:	signed 8 bit
ubyte:	unsigned 8 bit
sshort:	signed 16 bit
ushort:	unsigned 16 bit
sint:	signed 32 bit
uint:	unsigned 32 bit
slong:	signed 64 bit
ulong:	unsigned 64 bit
float:	floating point 32 bit
double:	floating point 64 bit
none:	no pixel type defined

│ │ │

crop

Crop a region of an image, the region is always clamped to the original image size in the sense that the given range is kept.. Supported parameters are:

Name	Type	Default	Description
end	streamable	[[4294967295,4294967295,4294967295]]	end of cropping range, maximum = (-1,-1,-1)
start	streamable	[[0,0,0]]	begin of cropping range

│ │ │

dilate

3d image stack dilate filter. Supported parameters are:

Name	Type	Default	Description
hint	string	black	a hint at the main image content (black\|white)
shape	factory	[sphere:r=2]	structuring element. For supported plug-ins see Plugin type: 3dimage/shape

│ │ │

│ │ │ @@ -63,33 +63,33 @@ │ │ │

│ │ │

erode

3d image stack erode filter. Supported parameters are:

Name	Type	Default	Description
hint	string	black	a hint at the main image content (black\|white)
shape	factory	[sphere:r=2]	structuring element. For supported plug-ins see Plugin type: 3dimage/shape

│ │ │

gauss

isotropic 3D gauss filter. Supported parameters are:

Name	Type	Default	Description
w	int in [0, inf)	1	filter width parameter

│ │ │

gradnorm

3D image to gradient norm filter. (This plug-in doesn't take parameters)

│ │ │

│ │ │ -

growmask

Use an input binary mask and a reference gray scale image to do region growing by adding the neighborhood pixels of an already added pixel if the have a lower intensity that is above the given threshold.. Supported parameters are:

Name	Type	Default	Description
min	float	1	lower threshold for mask growing
ref	io	(required,input)	reference image for mask region growing. For supported file types see Plugin type: 3dimage/io
shape	factory	6n	neighborhood mask. For supported plug-ins see Plugin type: 3dimage/shape

│ │ │ +

growmask

Name	Type	Default	Description
min	float	1	lower threshold for mask growing
ref	io	(input,required)	reference image for mask region growing. For supported file types see Plugin type: 3dimage/io
shape	factory	6n	neighborhood mask. For supported plug-ins see Plugin type: 3dimage/shape

│ │ │

invert

intensity invert filter. (This plug-in doesn't take parameters)

│ │ │

isovoxel

This filter scales an image to make the voxel size isometric and its size to correspond to the given value. Supported parameters are:

Name	Type	Default	Description
interp	factory	[bspline:d=3]	interpolation kernel to be used . For supported plug-ins see Plugin type: 1d/splinekernel
size	float in (0, inf)	1	isometric target voxel size

│ │ │

kmeans

3D image k-means filter. In the output image the pixel value represents the class membership and the class centers are stored as attribute in the image.. Supported parameters are:

Name	Type	Default	Description
c	int in [2, inf)	3	number of classes

│ │ │

label

A filter to label the connected components of a binary image.. Supported parameters are:

Name	Type	Default	Description
n	factory	6n	neighborhood mask. For supported plug-ins see Plugin type: 3dimage/shape

│ │ │

│ │ │ -

labelmap

Image filter to remap label id's. Only applicable to images with integer valued intensities/labels.. Supported parameters are:

Name	Type	Default	Description
map	string	(required,input)	Label mapping file

│ │ │ +

labelmap

Image filter to remap label id's. Only applicable to images with integer valued intensities/labels.. Supported parameters are:

Name	Type	Default	Description
map	string	(input,required)	Label mapping file

│ │ │

labelscale

Name	Type	Default	Description
out-size	3dbounds	(required)	target size given as two coma separated values

│ │ │

│ │ │ -

load

Load the input image from a file and use it to replace the current image in the pipeline.. Supported parameters are:

Name	Type	Default	Description
file	io	(required,input)	name of the input file to load from.. For supported file types see Plugin type: 3dimage/io

│ │ │ +

load

Load the input image from a file and use it to replace the current image in the pipeline.. Supported parameters are:

Name	Type	Default	Description
file	io	(input,required)	name of the input file to load from.. For supported file types see Plugin type: 3dimage/io

│ │ │

lvdownscale

This is a label voting downscale filter. It adownscales a 3D image by blocks. For each block the (non-zero) label that appears most times in the block is issued as output pixel in the target image. If two labels appear the same number of times, the one with the lower absolute value wins.. Supported parameters are:

Name	Type	Default	Description
b	3dbounds	[[1,1,1]]	blocksize for the downscaling. Each block will be represented by one pixel in the target image.

│ │ │

│ │ │ -

mask

Mask an image, one image is taken from the parameters list and the other from the normal filter input. Both images must be of the same dimensions and one must be binary. The attributes of the image coming through the filter pipeline are preserved. The output pixel type corresponds to the input image that is not binary.. Supported parameters are:

Name	Type	Default	Description
input	io	(required,input)	second input image file name. For supported file types see Plugin type: 3dimage/io

│ │ │ +

mask

Name	Type	Default	Description
input	io	(input,required)	second input image file name. For supported file types see Plugin type: 3dimage/io

│ │ │

mean

3D image mean filter. Supported parameters are:

Name	Type	Default	Description
w	int in [1, inf)	1	half filter width

│ │ │

median

median 3d filter. Supported parameters are:

Name	Type	Default	Description
w	int in [1, inf)	1	filter width parameter

│ │ │

mlv

Mean of Least Variance 3D image filter. Supported parameters are:

Name	Type	Default	Description
w	int in [1, inf)	1	filter width parameter

│ │ │

│ │ │ @@ -109,21 +109,21 @@ │ │ │

│ │ │

selectbig

A filter that creats a binary mask representing the intensity with the highest pixel count.The pixel value 0 will be ignored, and if two intensities have the same pixel count, then the result is undefined. The input pixel must have an integral pixel type.. (This plug-in doesn't take parameters)

│ │ │

sepconv

3D image intensity separaple convolution filter. Supported parameters are:

Name	Type	Default	Description
kx	factory	[gauss:w=1]	filter kernel in x-direction. For supported plug-ins see Plugin type: 1d/spacialkernel
ky	factory	[gauss:w=1]	filter kernel in y-direction. For supported plug-ins see Plugin type: 1d/spacialkernel
kz	factory	[gauss:w=1]	filter kernel in z-direction. For supported plug-ins see Plugin type: 1d/spacialkernel

│ │ │

sobel

Name

Type

Default

Description

dir

dict

Gradient direction
x:	gradient in x-direction
y:	gradient in y-direction
z:	gradient in z-direction

│ │ │

│ │ │ -

sws

seeded watershead. The algorithm extracts exactly so many reagions as initial labels are given in the seed image.. Supported parameters are:

Name	Type	Default	Description
grad	bool	0	Interpret the input image as gradient.
mark	bool	0	Mark the segmented watersheds with a special gray scale value
n	factory	[sphere:r=1]	Neighborhood for watershead region growing. For supported plug-ins see Plugin type: 3dimage/shape
seed	string	(required,input)	seed input image containing the lables for the initial regions

│ │ │ +

sws

seeded watershead. The algorithm extracts exactly so many reagions as initial labels are given in the seed image.. Supported parameters are:

Name	Type	Default	Description
grad	bool	0	Interpret the input image as gradient.
mark	bool	0	Mark the segmented watersheds with a special gray scale value
n	factory	[sphere:r=1]	Neighborhood for watershead region growing. For supported plug-ins see Plugin type: 3dimage/shape
seed	string	(input,required)	seed input image containing the lables for the initial regions

│ │ │

│ │ │ -

tee

Save the input image to a file and also pass it through to the next filter. Supported parameters are:

Name	Type	Default	Description
file	io	(required,output)	name of the output file to save the image too.. For supported file types see Plugin type: 3dimage/io

│ │ │ +

tee

Save the input image to a file and also pass it through to the next filter. Supported parameters are:

Name	Type	Default	Description
file	io	(output,required)	name of the output file to save the image too.. For supported file types see Plugin type: 3dimage/io

│ │ │

thinning

3D morphological thinning, based on: Lee and Kashyap, 'Building Skeleton Models via 3-D Medial Surface/Axis Thinning Algorithms', Graphical Models and Image Processing, 56(6):462-478, 1994. This implementation only supports the 26 neighbourhood.. (This plug-in doesn't take parameters)

│ │ │

│ │ │ -

transform

Transform the input image with the given transformation.. Supported parameters are:

Name	Type	Default	Description
file	io	(required,input)	Name of the file containing the transformation.. For supported file types see Plugin type: 3dtransform/io
imgboundary	factory		override image interpolation boundary conditions. For supported plug-ins see Plugin type: 1d/splinebc
imgkernel	factory		override image interpolator kernel. For supported plug-ins see Plugin type: 1d/splinekernel

│ │ │ +

transform

Transform the input image with the given transformation.. Supported parameters are:

Name	Type	Default	Description
file	io	(input,required)	Name of the file containing the transformation.. For supported file types see Plugin type: 3dtransform/io
imgboundary	factory		override image interpolation boundary conditions. For supported plug-ins see Plugin type: 1d/splinebc
imgkernel	factory		override image interpolator kernel. For supported plug-ins see Plugin type: 1d/splinekernel

│ │ │

variance

3D image variance filter. Supported parameters are:

Name	Type	Default	Description
w	int in [1, inf)	1	half filter width

│ │ │

ws

basic watershead segmentation.. Supported parameters are:

Name	Type	Default	Description
evalgrad	bool	0	Set to 1 if the input image does not represent a gradient norm image
mark	bool	0	Mark the segmented watersheds with a special gray scale value
n	factory	[sphere:r=1]	Neighborhood for watershead region growing. For supported plug-ins see Plugin type: 3dimage/shape
thresh	float in [0, 1)	0	Relative gradient norm threshold. The actual value threshold value is thresh * (max_grad - min_grad) + min_grad. Bassins separated by gradients with a lower norm will be joined

│ │ │

Plugin consumers:

│ │ │ mia-3dcost │ │ │ mia-3dimagefilter │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2davgmasked.html │ │ │ @@ -1,4 +1,4 @@ │ │ │ mia-2davgmasked

mia-2davgmasked
Prev	Analysis, filtering, combining, and segmentation of 2D images	Next

mia-2davgmasked

Sysnopis:

mia-2davgmasked {-i io} {-m io} [ │ │ │ options │ │ │ - ...]

Description:

Evaluate average intensities of an image seriesThis program is used to evaluate the average intensity and its variation of a series of images in a given masked region.

Options:

-i, --in-files=(required, input); io: input image(s). For supported file types see Plugin type: 2dimage/io
-m, --mask-file=(required, input); io: mask image, must be of type byte. For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

│ │ │ + ...]

Description:

Evaluate average intensities of an image seriesThis program is used to evaluate the average intensity and its variation of a series of images in a given masked region.

Options:

-i, --in-files=(input, required); io: input image(s). For supported file types see Plugin type: 2dimage/io
-m, --mask-file=(input, required); io: mask image, must be of type byte. For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

│ │ │

mia-2davgmasked

Author(s):

Gert Wollny

Prev	Up	Next
Analysis, filtering, combining, and segmentation of 2D images	Home	mia-2dbinarycombine

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dbinarycombine.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-2dbinarycombine

mia-2dbinarycombine
Prev	Analysis, filtering, combining, and segmentation of 2D images	Next

mia-2dbinarycombine

Sysnopis:

mia-2dbinarycombine {-1 io} {-2 io} {-o io} [ │ │ │ options │ │ │ - ...]

Description:

This program is used to combine two binary images by some kind of operation.

Options:

-1, --file1=(required, input); io

input mask image 1. For supported file types see Plugin type: 2dimage/io

-2, --file2=(required, input); io

input mask image 2. For supported file types see Plugin type: 2dimage/io

-o, --out-file=(required, output); io

output mask image. For supported file types see Plugin type: 2dimage/io

-p, --operation=nor; dict

Operation to be applied

or:	logocal or
nor:	logocal nor
and:	logocal and
nand:	logocal nand
xor:	logocal xor
nxor:	logocal nxor

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Combine the binary images b1.png and b2.png by using the 'nor' operation and store the result in b1nor2.png.

mia-2dbinarycombine -1 b1.png -2 b2.png -p nor -o b1nor2.png

Author(s):

Gert Wollny

Prev	Up	Next
mia-2davgmasked	Home	mia-2ddistance

│ │ │ + ...]

Description:

This program is used to combine two binary images by some kind of operation.

Options:

-1, --file1=(input, required); io

input mask image 1. For supported file types see Plugin type: 2dimage/io

-2, --file2=(input, required); io

input mask image 2. For supported file types see Plugin type: 2dimage/io

-o, --out-file=(output, required); io

output mask image. For supported file types see Plugin type: 2dimage/io

-p, --operation=nor; dict

Operation to be applied

or:	logocal or
nor:	logocal nor
and:	logocal and
nand:	logocal nand
xor:	logocal xor
nxor:	logocal nxor

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Combine the binary images b1.png and b2.png by using the 'nor' operation and store the result in b1nor2.png.

mia-2dbinarycombine -1 b1.png -2 b2.png -p nor -o b1nor2.png

Author(s):

Gert Wollny

Prev	Up	Next
mia-2davgmasked	Home	mia-2ddistance

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2ddeform.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-2ddeform

mia-2ddeform
Prev	Registration, Comparison, and Transformation of 2D images	Next

mia-2ddeform

Sysnopis:

mia-2ddeform {-i io} {-o io} {-t io} [ │ │ │ options │ │ │ - ...]

Description:

This program is used to deform a 2D image using a deformation vector field. Input image and deformation field must be of the same size. The transformation formula is 'x -> x - v(x)'

Options:

-i, --in-file=(required, input); io: input image. For supported file types see Plugin type: 2dimage/io
-o, --out-file=(required, output); io: transformed image. For supported file types see Plugin type: 2dimage/io
-t, --transformation=(required, input); io: transformation vector field. For supported file types see Plugin type: 2dvf/io
-p, --interpolator=bspline:d=3; factory: image interpolator kernel. For supported plug-ins see Plugin type: 1d/splinekernel

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Deform image input.png by using the transformation given in transform.v and store the result in deformed.png using linear interpolation

mia-2ddeform -i input.png -t transform.v -o deformed.png -p bspline:d=1

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dcost	Home	mia-2dfluid

│ │ │ + ...]

Description:

This program is used to deform a 2D image using a deformation vector field. Input image and deformation field must be of the same size. The transformation formula is 'x -> x - v(x)'

Options:

-i, --in-file=(input, required); io: input image. For supported file types see Plugin type: 2dimage/io
-o, --out-file=(output, required); io: transformed image. For supported file types see Plugin type: 2dimage/io
-t, --transformation=(input, required); io: transformation vector field. For supported file types see Plugin type: 2dvf/io
-p, --interpolator=bspline:d=3; factory: image interpolator kernel. For supported plug-ins see Plugin type: 1d/splinekernel

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Deform image input.png by using the transformation given in transform.v and store the result in deformed.png using linear interpolation

mia-2ddeform -i input.png -t transform.v -o deformed.png -p bspline:d=1

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dcost	Home	mia-2dfluid

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2ddistance.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-2ddistance

mia-2ddistance
Prev	Analysis, filtering, combining, and segmentation of 2D images	Next

mia-2ddistance

Sysnopis:

mia-2ddistance {-i io} {-d io} {-o string} [ │ │ │ options │ │ │ - ...]

Description:

This program evaluate the average or maximum distance of a mask given by a binary image to an image representing a distance map and prints the result to stdout. The distance map can be obtained by running the filter 'diatance' on a binary image.

Options:

-i, --in-file=(required, input); io

input image. For supported file types see Plugin type: 2dimage/io

-d, --distance-file=(required, input); io

distance field image (floating point). For supported file types see Plugin type: 2dimage/io

-o, --out-file=(required, output); string

output file, '-': write to stdout

-s, --scale=1; float

distance scaling factor

-m, --method=avg; dict

distance measuring method

avg:	use average
max:	use maximum
raw:	collect raw values as vector

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the maximum distance of mask m.v by using the distance field distance.v and scale by factor 2.0. The result is written to stdout

mia-2ddistance -i m.v -d distance.v -s 2.0 -m max

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dbinarycombine	Home	mia-2dfuzzysegment

│ │ │ + ...]

Description:

Options:

-i, --in-file=(input, required); io

input image. For supported file types see Plugin type: 2dimage/io

-d, --distance-file=(input, required); io

distance field image (floating point). For supported file types see Plugin type: 2dimage/io

-o, --out-file=(output, required); string

output file, '-': write to stdout

-s, --scale=1; float

distance scaling factor

-m, --method=avg; dict

distance measuring method

avg:	use average
max:	use maximum
raw:	collect raw values as vector

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the maximum distance of mask m.v by using the distance field distance.v and scale by factor 2.0. The result is written to stdout

mia-2ddistance -i m.v -d distance.v -s 2.0 -m max

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dbinarycombine	Home	mia-2dfuzzysegment

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2devaltransformquantity.html │ │ │ @@ -14,9 +14,9 @@ │ │ │ style=sparse #storage style (sparse|grid) │ │ │ repn=float32 #representation of values │ │ │ size=1000 1000 #grid size of the transformation │ │ │ endian=low #endianess of binary data (low|big) │ │ │ } │ │ │ │ │ │ This example header has to be interpreted like follows: two-dimensional data, each entry consists of 7 values the values etry consists of a 2D vector, a scalar, and a 2x2 matrix (saved in row-major format).The data records represent strain tensors, and only a sparse set of points is given. The values are given as single floating point (32 bit). The original transformation field corresponds to images of 1000x1000 pixels and the binary data is stored in low endian format.

Options:

│ │ │ -File-IO

-i, --in-file=(required, input); string: input point set, if this parameter is given a sparse evaluation of the quantity will be done, otherwise the quantity is evaluated for each grid point of the transformation range.
-o, --out-file=(required, output); string: output strains file, for a format description see above.
-t, --transformation=(required, input); io: transformation of which the quantity will be evaluated.. For supported file types see Plugin type: 2dtransform/io

│ │ │ +File-IO

-i, --in-file=(input, required); string: input point set, if this parameter is given a sparse evaluation of the quantity will be done, otherwise the quantity is evaluated for each grid point of the transformation range.
-o, --out-file=(output, required); string: output strains file, for a format description see above.
-t, --transformation=(input, required); io: transformation of which the quantity will be evaluated.. For supported file types see Plugin type: 2dtransform/io

│ │ │ Parameters

-q, --quantity=strain; dict

Specify the quantity to be evaluated at the given points

derivative:	Evaluate the transformation derivative at the given points
strain:	Evaluate the strain tensor at the given points

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Derivative of the transformation change.v2df for each point given in input.csv are evaluated and written to output.s.

mia-2deval-transformquantity -i input.csv -o output.s --transformation change.v2df

Author(s):

Gert Wollny

Prev	Up	Next
Tools for the Analysis of 2D image series	Home	mia-2dtrackpixelmovement

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dfluid.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-2dfluid

mia-2dfluid
Prev	Registration, Comparison, and Transformation of 2D images	Next

mia-2dfluid

Sysnopis:

mia-2dfluid {-i io} {-r io} [ │ │ │ options │ │ │ - ...]

Description:

This program is used for non-rigid registration based on fluid dynamics. For reference see

Wollny, G. and Kruggel, F., 'Computational cost of non-rigid registration algorithms based on fluid dynamics', IEEE Transactions on Medical Imaging, 11(8), pp. 946-952, 2002.

It uses SSD as the sole registration criterion.

Options:

File-IO

-i, --in-image=(required, input); io: input (test) image to be registered. For supported file types see Plugin type: 2dimage/io
-r, --ref-image=(required, input); io: reference image. For supported file types see Plugin type: 2dimage/io
-o, --out-transformation=(output); io: output transformation comprising the registration. For supported file types see Plugin type: 2dvf/io
-d, --out-image=(output); io: output image deformed according to the transformation. For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Registration parameters

-m, --mgstart=16; uint: multigrid start size
-e, --epsilon=0.001; float: optimization breaking condition
--mu=1; float: elasticity parameter
--lambda=1; float: elasticity parameter
--elastic: use elastic registration

Example:

Register image test.v to image ref.v and write the deformation vector field regfield.v. Start registration at the smallest size above 16 pixel.

mia-2dfluid -i test.v -r ref.v -o regfield.v -s 16

Author(s):

Gert Wollny

Prev	Up	Next
mia-2ddeform	Home	mia-2dfluid-syn-registration

│ │ │ + ...]

Description:

This program is used for non-rigid registration based on fluid dynamics. For reference see

Wollny, G. and Kruggel, F., 'Computational cost of non-rigid registration algorithms based on fluid dynamics', IEEE Transactions on Medical Imaging, 11(8), pp. 946-952, 2002.

It uses SSD as the sole registration criterion.

Options:

File-IO

-i, --in-image=(input, required); io: input (test) image to be registered. For supported file types see Plugin type: 2dimage/io
-r, --ref-image=(input, required); io: reference image. For supported file types see Plugin type: 2dimage/io
-o, --out-transformation=(output); io: output transformation comprising the registration. For supported file types see Plugin type: 2dvf/io
-d, --out-image=(output); io: output image deformed according to the transformation. For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Registration parameters

-m, --mgstart=16; uint: multigrid start size
-e, --epsilon=0.001; float: optimization breaking condition
--mu=1; float: elasticity parameter
--lambda=1; float: elasticity parameter
--elastic: use elastic registration

Example:

Register image test.v to image ref.v and write the deformation vector field regfield.v. Start registration at the smallest size above 16 pixel.

mia-2dfluid -i test.v -r ref.v -o regfield.v -s 16

Author(s):

Gert Wollny

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mia-2ddeform	Home	mia-2dfluid-syn-registration

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dfluidsynregistration.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-2dfluid-syn-registration

mia-2dfluid-syn-registration
Prev	Registration, Comparison, and Transformation of 2D images	Next

mia-2dfluid-syn-registration

Sysnopis:

mia-2dfluid-syn-registration {-i io} {-r io} {-o io} {-O io} [ │ │ │ options │ │ │ - ...]

Description:

This program implements the registration of two gray scale 2D images. The transformation applied is a symmeric diffeomorpic fluid dynamic registration. To work most efficiently, this program makes a few assumptions about the imput data, i.e. the image must be of the same size, have the same voxel spacing, and any intensity range normalization or equalization should also be done before calling this program.

Options:

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

IO

-i, --in-image=(required, input); io: test image. For supported file types see Plugin type: 2dimage/io
-r, --ref-image=(required, input); io: reference image. For supported file types see Plugin type: 2dimage/io
-o, --transform=(required, output); io: output transformation. For supported file types see Plugin type: 2dtransform/io
-O, --inverse-transform=(required, output); io: inverse output transformation. For supported file types see Plugin type: 2dtransform/io

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Registration

-l, --mg-levels=3; uint: Number of multi-resolution levels to run the registration on. Not that some registration parameters can be given as a coma seperated list to indicate per level values. In these cases if the number of given values is smaller than the number of multi-resolution levels (this parameter), the the last given value is used for all subsequest multi-resolution levels.
-S, --step=0.25; float in (0, 0.5]: Initial step size for all levels
-c, --cost=ssd; factory: Image similarity function to be minimized. For supported plug-ins see Plugin type: 2dimage/cost
-R, --regularizer=sor:kernel=fluid,maxiter=50; factory: Regularization for the force to transformation update. For supported plug-ins see Plugin type: 2dvf/regularizer
-T, --conv-test-interval= in [4, 40]: Convergence test interations intervall: In order to measure convergence the cost function value is averaged over this amount of iterations, and the decline rate is evaluated based on the linare regression of the cost function values in this intervall. This parameter can be given as a coma-seperated list with values corresponding to the multi-resolution levels, see option --mg-levels for more information.
-D, --stop-decline-rate= in [0, inf): Stopping criterium for registration based on the cost decline rate. If the rate below this value, the iteration is stopped. This parameter can be given as a coma-seperated list with values corresponding to the multi-resolution levels, see option --mg-levels for more information.
-C, --stop-cost=: Stopping criterium for registration based on the cost value. If the cost drops below this value, the iteration is stopped. This parameter can be given as a coma-seperated list with values corresponding to the multi-resolution levels, see option --mg-levels for more information.
-I, --iter= in [4, inf): Naximum number if iterations done on each multi-resolution level. This parameter can be given as a coma-seperated list with values corresponding to the multi-resolution levels, see option --mg-levels for more information.

Example:

Register image test.v to image ref.v saving the transformation to transform.v and the inverse transform to inverse-transform.v. Use three multiresolution levels, ssd as image cost function.

mia-2dfluid-syn-registration -i test.v -r ref.v -t transform.v -T inverse-transform.v  -l 3 ssd

Author(s):

Gert Wollny

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mia-2dfluid	Home	mia-2dforce

│ │ │ + ...]

Description:

Options:

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

IO

-i, --in-image=(input, required); io: test image. For supported file types see Plugin type: 2dimage/io
-r, --ref-image=(input, required); io: reference image. For supported file types see Plugin type: 2dimage/io
-o, --transform=(output, required); io: output transformation. For supported file types see Plugin type: 2dtransform/io
-O, --inverse-transform=(output, required); io: inverse output transformation. For supported file types see Plugin type: 2dtransform/io

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Registration

-l, --mg-levels=3; uint: Number of multi-resolution levels to run the registration on. Not that some registration parameters can be given as a coma seperated list to indicate per level values. In these cases if the number of given values is smaller than the number of multi-resolution levels (this parameter), the the last given value is used for all subsequest multi-resolution levels.
-S, --step=0.25; float in (0, 0.5]: Initial step size for all levels
-c, --cost=ssd; factory: Image similarity function to be minimized. For supported plug-ins see Plugin type: 2dimage/cost
-R, --regularizer=sor:kernel=fluid,maxiter=50; factory: Regularization for the force to transformation update. For supported plug-ins see Plugin type: 2dvf/regularizer
-T, --conv-test-interval= in [4, 40]: Convergence test interations intervall: In order to measure convergence the cost function value is averaged over this amount of iterations, and the decline rate is evaluated based on the linare regression of the cost function values in this intervall. This parameter can be given as a coma-seperated list with values corresponding to the multi-resolution levels, see option --mg-levels for more information.
-D, --stop-decline-rate= in [0, inf): Stopping criterium for registration based on the cost decline rate. If the rate below this value, the iteration is stopped. This parameter can be given as a coma-seperated list with values corresponding to the multi-resolution levels, see option --mg-levels for more information.
-C, --stop-cost=: Stopping criterium for registration based on the cost value. If the cost drops below this value, the iteration is stopped. This parameter can be given as a coma-seperated list with values corresponding to the multi-resolution levels, see option --mg-levels for more information.
-I, --iter= in [4, inf): Naximum number if iterations done on each multi-resolution level. This parameter can be given as a coma-seperated list with values corresponding to the multi-resolution levels, see option --mg-levels for more information.

Example:

Register image test.v to image ref.v saving the transformation to transform.v and the inverse transform to inverse-transform.v. Use three multiresolution levels, ssd as image cost function.

mia-2dfluid-syn-registration -i test.v -r ref.v -t transform.v -T inverse-transform.v  -l 3 ssd

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dfluid	Home	mia-2dforce

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dforce.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-2dforce

mia-2dforce
Prev	Registration, Comparison, and Transformation of 2D images	Next

mia-2dforce

Sysnopis:

mia-2dforce {-i io} {-r io} {-o io} {-c string} [ │ │ │ options │ │ │ - ...]

Description:

This image evaluate the force field between two images based on a given cost function.

Options:

-i, --src-file=(required, input); io: input image. For supported file types see Plugin type: 2dimage/io
-r, --ref-file=(required, input); io: reference image. For supported file types see Plugin type: 2dimage/io
-o, --out-file=(required, output); io: output force norm image. For supported file types see Plugin type: 2dimage/io
-c, --cost=(required); string: cost function to use

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the force between test.v and reference.v by using SSD ans save the norm of the force to forcenorm.v

mia-2dforce -i test.v -r reference.v -c ssd -o forcenorm.v

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dfluid-syn-registration	Home	mia-2dimageregistration

│ │ │ + ...]

Description:

This image evaluate the force field between two images based on a given cost function.

Options:

-i, --src-file=(input, required); io: input image. For supported file types see Plugin type: 2dimage/io
-r, --ref-file=(input, required); io: reference image. For supported file types see Plugin type: 2dimage/io
-o, --out-file=(output, required); io: output force norm image. For supported file types see Plugin type: 2dimage/io
-c, --cost=(required); string: cost function to use

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the force between test.v and reference.v by using SSD ans save the norm of the force to forcenorm.v

mia-2dforce -i test.v -r reference.v -c ssd -o forcenorm.v

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dfluid-syn-registration	Home	mia-2dimageregistration

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dfuzzysegment.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-2dfuzzysegment

mia-2dfuzzysegment
Prev	Analysis, filtering, combining, and segmentation of 2D images	Next

mia-2dfuzzysegment

Sysnopis:

mia-2dfuzzysegment {-i io} [ │ │ │ options │ │ │ - ...]

Description:

This program runs a combined fuzzy c-means clustering and B-field correction to facilitate a fuzzy segmentation of 2D image. cf D.L. Pham and J.L.Prince, "An adaptive fuzzy C-means algorithm for image segmentation in the presence of intensity inhomogeneities", Pat. Rec. Let., 20:57-68,1999

Options:

File-IO

-i, --in-file=(required, input); io: input image(s) to be segmenetd. For supported file types see Plugin type: 2dimage/io
-c, --cls-file=(output); io: output class probability images (floating point values and multi-image). For supported file types see Plugin type: 2dimage/io
-o, --b0-file=(output); io: image corrected for intensity non-uniformity. For supported file types see Plugin type: 2dimage/io
-g, --gain-file=(output); io: gain field (floating point valued). For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Parameters

-n, --no-of-classes=3; int: number of classes
-r, --residuum=0.1; float: relative residuum
--l1=200000; float: Penalize magnitude of intensity inhomogeinity correction
--l2=2e+06; float: Smoothness of intensity inhomogeinity correction

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run a 5-class segmentation over input image input.v and store the class probability images in cls.v and the B0-field corrected image in b0.v.

mia-2dfuzzysegment -i input.v -c 5 -o b0.v -c cls.v

Author(s):

Gert Wollny

Prev	Up	Next
mia-2ddistance	Home	mia-2dgrayimage-combine-to-rgb

│ │ │ + ...]

Description:

Options:

File-IO

-i, --in-file=(input, required); io: input image(s) to be segmenetd. For supported file types see Plugin type: 2dimage/io
-c, --cls-file=(output); io: output class probability images (floating point values and multi-image). For supported file types see Plugin type: 2dimage/io
-o, --b0-file=(output); io: image corrected for intensity non-uniformity. For supported file types see Plugin type: 2dimage/io
-g, --gain-file=(output); io: gain field (floating point valued). For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Parameters

-n, --no-of-classes=3; int: number of classes
-r, --residuum=0.1; float: relative residuum
--l1=200000; float: Penalize magnitude of intensity inhomogeinity correction
--l2=2e+06; float: Smoothness of intensity inhomogeinity correction

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run a 5-class segmentation over input image input.v and store the class probability images in cls.v and the B0-field corrected image in b0.v.

mia-2dfuzzysegment -i input.v -c 5 -o b0.v -c cls.v

Author(s):

Gert Wollny

Prev	Up	Next
mia-2ddistance	Home	mia-2dgrayimage-combine-to-rgb

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dgrayimagecombinetorgb.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-2dgrayimage-combine-to-rgb

mia-2dgrayimage-combine-to-rgb
Prev	Analysis, filtering, combining, and segmentation of 2D images	Next

mia-2dgrayimage-combine-to-rgb

Sysnopis:

mia-2dgrayimage-combine-to-rgb {-o io} [ │ │ │ options │ │ │ - ...]

Description:

This program combines up to three gray scale image to a three channel RGB image with eight bit per color channel. The input images must be gray scale of eight bit colordepth. If at input one channel is not given, it will be set to zero. at least one input channel must be given.

Options:

-b, --blue=(input); io: input image for blue channel. For supported file types see Plugin type: 2dimage/io
-g, --green=(input); io: input image for green channel. For supported file types see Plugin type: 2dimage/io
-r, --red=(input); io: input image for red channel. For supported file types see Plugin type: 2dimage/io
-o, --out-file=(required, output); io: combined output image. For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Combine the images red.png, blue.tiff, and green.bmp to the output image rgb.jpg.

mia-2dgrayimage-combine-to-rgb -r red.png -b blue.tiff -g green.bmp -o rgb.jpg

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dfuzzysegment	Home	mia-2dimagecombine-dice

│ │ │ + ...]

Description:

Options:

-b, --blue=(input); io: input image for blue channel. For supported file types see Plugin type: 2dimage/io
-g, --green=(input); io: input image for green channel. For supported file types see Plugin type: 2dimage/io
-r, --red=(input); io: input image for red channel. For supported file types see Plugin type: 2dimage/io
-o, --out-file=(output, required); io: combined output image. For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Combine the images red.png, blue.tiff, and green.bmp to the output image rgb.jpg.

mia-2dgrayimage-combine-to-rgb -r red.png -b blue.tiff -g green.bmp -o rgb.jpg

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dfuzzysegment	Home	mia-2dimagecombine-dice

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dgroundtruthreg.html │ │ │ @@ -1,7 +1,7 @@ │ │ │ mia-2dgroundtruthreg

mia-2dgroundtruthreg
Prev	Registration of series of 2D images	Next

mia-2dgroundtruthreg

Sysnopis:

mia-2dgroundtruthreg {-i string} {-o string} {-A double} {-B double} {-R double} [ │ │ │ options │ │ │ ...]

Description:

This program implements the non-linear registration based on Pseudo Ground Thruth for motion compensation of series of myocardial perfusion images as described in

Chao Li and Ying Sun, 'Nonrigid Registration of Myocardial Perfusion MRI Using Pseudo Ground Truth' , In Proc. Medical Image Computing and Computer-Assisted Intervention MICCAI 2009, 165-172, 2009.

Note that for this nonlinear motion correction a preceding linear registration step is usually required.

Options:

│ │ │ -File-IO

-i, --in-file=(required, input); string: input perfusion data set
-o, --out-file=(required, output); string: output perfusion data set
-r, --registered=reg; stringSTRING: file name base for registered files

│ │ │ +File-IO

-i, --in-file=(input, required); string: input perfusion data set
-o, --out-file=(output, required); string: output perfusion data set
-r, --registered=reg; stringSTRING: file name base for registered files

│ │ │ Preconditions

-s, --skip=2; ulong: skip images at beginning of series
-P, --passes=4; ulong: number of registration passes

│ │ │ Pseudo-Ground-Thruth

-A, --alpha=(required); double: spacial neighborhood penalty weight
-B, --beta=(required); double: temporal second derivative penalty weight
-R, --rho_thresh=(required); double: correlation threshold for neighborhood analysis

│ │ │ Registration

-O, --optimizer=gsl:opt=gd,step=0.1; factory: Optimizer used for minimization. For supported plug-ins see Plugin type: minimizer/singlecost
-p, --interpolator=bspline:d=3; factory: image interpolator kernel. For supported plug-ins see Plugin type: 1d/splinekernel
-l, --mr-levels=3; ulong: multi-resolution levels
-d, --divcurl=20; double: divcurl regularization weight
--divcurl-divider=4; double: divcurl weight scaling with each new pass
-a, --start-c-rate=32; ulong: start coefficinet rate in spines, gets divided by --c-rate-divider with every pass
--c-rate-divider=4; double: cofficient rate divider for each pass
-w, --imageweight=1; double: image cost weight

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Register the perfusion series given by images imageXXXX.exr by using Pseudo Ground Truth estimation. Skip two images at the beginning and otherwiese use the default parameters. Store the result images to 'regXXXX.exr'.

mia-2dgroundtruthreg -i imageXXXX.exr -o regXXXX.exr -k 2

Author(s):

Gert Wollny

Prev	Up	Next
Registration of series of 2D images	Home	mia-2dmany2one-nonrigid

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dimagecombinedice.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-2dimagecombine-dice

mia-2dimagecombine-dice
Prev	Analysis, filtering, combining, and segmentation of 2D images	Next

mia-2dimagecombine-dice

Sysnopis:

mia-2dimagecombine-dice {-1 io} {-2 io} [ │ │ │ options │ │ │ - ...]

Description:

This program evaluate the dice index of two binary masks given as binary images. The result is written to stdout.

Options:

-1, --in-file-1=(required, input); io: input image 1. For supported file types see Plugin type: 2dimage/io
-2, --in-file-2=(required, input); io: input image 2. For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the dice index of maks1.png and mask2.png

mia-2dimagecombine-dice -1 mask1.png -2 mask2.png

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dgrayimage-combine-to-rgb	Home	mia-2dimagecombiner

│ │ │ + ...]

Description:

This program evaluate the dice index of two binary masks given as binary images. The result is written to stdout.

Options:

-1, --in-file-1=(input, required); io: input image 1. For supported file types see Plugin type: 2dimage/io
-2, --in-file-2=(input, required); io: input image 2. For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the dice index of maks1.png and mask2.png

mia-2dimagecombine-dice -1 mask1.png -2 mask2.png

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dgrayimage-combine-to-rgb	Home	mia-2dimagecombiner

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dimagecombiner.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-2dimagecombiner

mia-2dimagecombiner
Prev	Analysis, filtering, combining, and segmentation of 2D images	Next

mia-2dimagecombiner

Sysnopis:

mia-2dimagecombiner {-1 io} {-2 io} {-o io} [ │ │ │ options │ │ │ - ...]

Description:

Combine two image by a given operation.

Options:

-1, --in-file-1=(required, input); io: first input image to be combined. For supported file types see Plugin type: 2dimage/io
-2, --in-file-2=(required, input); io: second input image to be combined. For supported file types see Plugin type: 2dimage/io
-o, --out-file=(required, output); io: output image(s) that have been filtered. For supported file types see Plugin type: 2dimage/io
-p, --operation=absdiff; factory: operation to be applied. For supported plug-ins see Plugin type: 2dimage/combiner

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Combine image A.exr and image B.exr by adding the intensity values and save the output to sum.exr.

mia-2dimagecombiner -i A.exr -r B.exr -o sum.exr -p add

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dimagecombine-dice	Home	mia-2dimagecreator

│ │ │ + ...]

Description:

Combine two image by a given operation.

Options:

-1, --in-file-1=(input, required); io: first input image to be combined. For supported file types see Plugin type: 2dimage/io
-2, --in-file-2=(input, required); io: second input image to be combined. For supported file types see Plugin type: 2dimage/io
-o, --out-file=(output, required); io: output image(s) that have been filtered. For supported file types see Plugin type: 2dimage/io
-p, --operation=absdiff; factory: operation to be applied. For supported plug-ins see Plugin type: 2dimage/combiner

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Combine image A.exr and image B.exr by adding the intensity values and save the output to sum.exr.

mia-2dimagecombiner -i A.exr -r B.exr -o sum.exr -p add

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dimagecombine-dice	Home	mia-2dimagecreator

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dimagecreator.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-2dimagecreator

mia-2dimagecreator
Prev	Analysis, filtering, combining, and segmentation of 2D images	Next

mia-2dimagecreator

Sysnopis:

mia-2dimagecreator {-o io} {-j factory} [ │ │ │ options │ │ │ - ...]

Description:

This program is used to create test images.

Options:

-o, --out-file=(required, output); io

output file for create object. For supported file types see Plugin type: 2dimage/io

-s, --size=[128,128]; 2dbounds

size of the object

-r, --repn=ubyte; dict

input pixel type

bit:	binary data
sbyte:	signed 8 bit
ubyte:	unsigned 8 bit
sshort:	signed 16 bit
ushort:	unsigned 16 bit
sint:	signed 32 bit
uint:	unsigned 32 bit
slong:	signed 64 bit
ulong:	unsigned 64 bit
float:	floating point 32 bit
double:	floating point 64 bit
none:	no pixel type defined

-j, --object=(required); factory

object to be created. For supported plug-ins see Plugin type: 2dimage/creator

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Create a 2D image containing a lattic with standard parameters of size <64,128> and pixel type 'float' and save the result to lattic.v

mia-2dimagecreator -o lattic.v -s '<64,128>' -r float -j lattic

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dimagecombiner	Home	mia-2dimagefilter

│ │ │ + ...]

Description:

This program is used to create test images.

Options:

-o, --out-file=(output, required); io

output file for create object. For supported file types see Plugin type: 2dimage/io

-s, --size=[128,128]; 2dbounds

size of the object

-r, --repn=ubyte; dict

input pixel type

bit:	binary data
sbyte:	signed 8 bit
ubyte:	unsigned 8 bit
sshort:	signed 16 bit
ushort:	unsigned 16 bit
sint:	signed 32 bit
uint:	unsigned 32 bit
slong:	signed 64 bit
ulong:	unsigned 64 bit
float:	floating point 32 bit
double:	floating point 64 bit
none:	no pixel type defined

-j, --object=(required); factory

object to be created. For supported plug-ins see Plugin type: 2dimage/creator

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Create a 2D image containing a lattic with standard parameters of size <64,128> and pixel type 'float' and save the result to lattic.v

mia-2dimagecreator -o lattic.v -s '<64,128>' -r float -j lattic

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dimagecombiner	Home	mia-2dimagefilter

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dimagefilter.html │ │ │ @@ -2,8 +2,8 @@ │ │ │ options │ │ │ ...] [ │ │ │ │ │ │ Plugin type: 2dimage/filter │ │ │ │ │ │ ...]

Description:

This program runs a series filters on a given input image. The filters are given as extra parameters on the command line and Ware run in the order in which they are given. To obtain a list of available filters you may run │ │ │ 'mia-plugin-help filter/2dimage' │ │ │ -from the command line

Options:

-i, --in-file=(required, input); io: input image(s) to be filtered. For supported file types see Plugin type: 2dimage/io
-o, --out-file=(required, output); io: output image(s) that have been filtered. For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run a kmeans classification of 5 classes on input.png and then a binarization of the 4th class and store the result in result.png

mia-2dimagefilter -i input.png -o result.png kmeans:c=5 binarize:min=4,max=4

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dimagecreator	Home	mia-2dimagefilterstack

│ │ │ +from the command line

Options:

-i, --in-file=(input, required); io: input image(s) to be filtered. For supported file types see Plugin type: 2dimage/io
-o, --out-file=(output, required); io: output image(s) that have been filtered. For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run a kmeans classification of 5 classes on input.png and then a binarization of the 4th class and store the result in result.png

mia-2dimagefilter -i input.png -o result.png kmeans:c=5 binarize:min=4,max=4

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dimagecreator	Home	mia-2dimagefilterstack

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dimagefilterstack.html │ │ │ @@ -1,7 +1,7 @@ │ │ │ mia-2dimagefilterstack

mia-2dimagefilterstack
Prev	Analysis, filtering, combining, and segmentation of 2D images	Next

mia-2dimagefilterstack

Sysnopis:

mia-2dimagefilterstack {-i io} {-o io} [ │ │ │ options │ │ │ ...] [ │ │ │ │ │ │ Plugin type: 2dimage/filter │ │ │ │ │ │ - ...]

Description:

This program runs a series filters on a series of consecutive numbered input image. The filters are given as extra parameters on the command line and are run in the order in which they are given.

Options:

File IO

-i, --in-file=(required, input); io: input image(s) to be filtered. For supported file types see Plugin type: 2dimage/io
-o, --out-file=(required, output); io: output file name base, the file type is set accurding to the 'type' option. For supported file types see Plugin type: 2dimage/io
-t, --type=: output file type, if not given the input type is used Supported values are:(-, @, BMP, DCM, EXR, JPEG, JPG, PNG, RAW, TIF, TIFF, V, VISTA, bmp, dcm, exr, jpeg, jpg, png, raw, tif, tiff, v, vista, )

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Processing1

-s, --start=0; ulong: first possible number of file number range to be filtered
-e, --end=2147483647; ulong: last possible number of file number range to be filtered

Example:

Run a kmeans classification of 5 classes on images inputXXXX.png (X being digits) and then a binarization of the 4th class and store the result in resultXXXX.png

mia-2dimagefilterstack -i input0000.png -o result -t png kmeans:c=5 binarize:min=4,max=4

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dimagefilter	Home	mia-2dimagefullstats

│ │ │ + ...]

Description:

This program runs a series filters on a series of consecutive numbered input image. The filters are given as extra parameters on the command line and are run in the order in which they are given.

Options:

File IO

-i, --in-file=(input, required); io: input image(s) to be filtered. For supported file types see Plugin type: 2dimage/io
-o, --out-file=(output, required); io: output file name base, the file type is set accurding to the 'type' option. For supported file types see Plugin type: 2dimage/io
-t, --type=: output file type, if not given the input type is used Supported values are:(-, @, BMP, DCM, EXR, JPEG, JPG, PNG, RAW, TIF, TIFF, V, VISTA, bmp, dcm, exr, jpeg, jpg, png, raw, tif, tiff, v, vista, )

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Processing1

-s, --start=0; ulong: first possible number of file number range to be filtered
-e, --end=2147483647; ulong: last possible number of file number range to be filtered

Example:

Run a kmeans classification of 5 classes on images inputXXXX.png (X being digits) and then a binarization of the 4th class and store the result in resultXXXX.png

mia-2dimagefilterstack -i input0000.png -o result -t png kmeans:c=5 binarize:min=4,max=4

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dimagefilter	Home	mia-2dimagefullstats

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dimagefullstats.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-2dimagefullstats

mia-2dimagefullstats
Prev	Analysis, filtering, combining, and segmentation of 2D images	Next

mia-2dimagefullstats

Sysnopis:

mia-2dimagefullstats {-i io} [ │ │ │ options │ │ │ - ...]

Description:

This progranm is used to evaluate some statistics of an image. Output is Mean, Variation, Median, Min and Max of the intensity values.

Options:

-i, --in-file=(required, input); io: input image. For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the statistics of image input.png

mia-2dimagefullstats -i input.png

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dimagefilterstack	Home	mia-2dimageseries-maximum-intensity-projection

│ │ │ + ...]

Description:

This progranm is used to evaluate some statistics of an image. Output is Mean, Variation, Median, Min and Max of the intensity values.

Options:

-i, --in-file=(input, required); io: input image. For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the statistics of image input.png

mia-2dimagefullstats -i input.png

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dimagefilterstack	Home	mia-2dimageseries-maximum-intensity-projection

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dimageregistration.html │ │ │ @@ -1,7 +1,7 @@ │ │ │ mia-2dimageregistration

mia-2dimageregistration
Prev	Registration, Comparison, and Transformation of 2D images	Next

mia-2dimageregistration

Sysnopis:

mia-2dimageregistration {-i io} {-r io} {-t io} [ │ │ │ options │ │ │ ...] [ │ │ │ │ │ │ Plugin type: 2dimage/fullcost │ │ │ │ │ │ - ...]

Description:

This program runs registration of two images optimizing a transformation of the given transformation model by optimizing certain cost measures that are given as free parameters.

Options:

File-IO

-i, --in-image=(required, input); io: test image to be registered. For supported file types see Plugin type: 2dimage/io
-r, --ref-image=(required, input); io: reference image to be registered to. For supported file types see Plugin type: 2dimage/io
-o, --out-image=(output); io: registered output image. For supported file types see Plugin type: 2dimage/io
-t, --transformation=(required, output); io: output transformation comprising the registration. For supported file types see Plugin type: 2dtransform/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Parameters

-l, --levels=3; ulong: multi-resolution levels
-O, --optimizer=gsl:opt=gd,step=0.1; factory: Optimizer used for minimization. For supported plug-ins see Plugin type: minimizer/singlecost
-R, --refiner=: optimizer used for refinement after the main optimizer was called. For supported plug-ins see Plugin type: minimizer/singlecost
-f, --transForm=spline; factory: transformation type. For supported plug-ins see Plugin type: 2dimage/transform

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Register the image 'moving.png' to the image 'reference.png' by using a rigid transformation model and ssd as cost function. Write the result to output.png

mia-2dimageregistration   -i moving.png -r reference.png -o output.png -f rigid image:cost=ssd

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dforce	Home	mia-2dmulti-force

│ │ │ + ...]

Description:

This program runs registration of two images optimizing a transformation of the given transformation model by optimizing certain cost measures that are given as free parameters.

Options:

File-IO

-i, --in-image=(input, required); io: test image to be registered. For supported file types see Plugin type: 2dimage/io
-r, --ref-image=(input, required); io: reference image to be registered to. For supported file types see Plugin type: 2dimage/io
-o, --out-image=(output); io: registered output image. For supported file types see Plugin type: 2dimage/io
-t, --transformation=(output, required); io: output transformation comprising the registration. For supported file types see Plugin type: 2dtransform/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Parameters

-l, --levels=3; ulong: multi-resolution levels
-O, --optimizer=gsl:opt=gd,step=0.1; factory: Optimizer used for minimization. For supported plug-ins see Plugin type: minimizer/singlecost
-R, --refiner=: optimizer used for refinement after the main optimizer was called. For supported plug-ins see Plugin type: minimizer/singlecost
-f, --transForm=spline; factory: transformation type. For supported plug-ins see Plugin type: 2dimage/transform

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Register the image 'moving.png' to the image 'reference.png' by using a rigid transformation model and ssd as cost function. Write the result to output.png

mia-2dimageregistration   -i moving.png -r reference.png -o output.png -f rigid image:cost=ssd

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dforce	Home	mia-2dmulti-force

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dimageselect.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-2dimageselect

mia-2dimageselect
Prev	Image conversion	Next

mia-2dimageselect

Sysnopis:

mia-2dimageselect {-i io} {-o io} [ │ │ │ options │ │ │ - ...]

Description:

This program is used to select one 2D images from a multi-image file.

Options:

-i, --in-file=(required, input); io: input images. For supported file types see Plugin type: 2dimage/io
-o, --out-file=(required, output); io: output image. For supported file types see Plugin type: 2dimage/io
-n, --number=0; ulong: image number to be selected

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Store the third image in multiimage.v to image.v (note: counting starts with zero).

mia-2dimageselect -i multiimage.v -o image.v -n 2

Author(s):

Gert Wollny

Prev	Up	Next
Image conversion	Home	mia-2dmultiimageto3d

│ │ │ + ...]

Description:

This program is used to select one 2D images from a multi-image file.

Options:

-i, --in-file=(input, required); io: input images. For supported file types see Plugin type: 2dimage/io
-o, --out-file=(output, required); io: output image. For supported file types see Plugin type: 2dimage/io
-n, --number=0; ulong: image number to be selected

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Store the third image in multiimage.v to image.v (note: counting starts with zero).

mia-2dimageselect -i multiimage.v -o image.v -n 2

Author(s):

Gert Wollny

Prev	Up	Next
Image conversion	Home	mia-2dmultiimageto3d

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dimageseriesmaximumintensityprojection.html │ │ │ @@ -1,4 +1,4 @@ │ │ │ mia-2dimageseries-maximum-intensity-projection

mia-2dimageseries-maximum-intensity-projection
Prev	Analysis, filtering, combining, and segmentation of 2D images	Next

mia-2dimageseries-maximum-intensity-projection

Sysnopis:

mia-2dimageseries-maximum-intensity-projection {-o io} [ │ │ │ options │ │ │ - ...]

Description:

This program is used to evaluate the per-pixel maximum intensity of an image series.

Options:

-o, --out-file=(required, output); io: output image. For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

│ │ │ + ...]

Description:

This program is used to evaluate the per-pixel maximum intensity of an image series.

Options:

-o, --out-file=(output, required); io: output image. For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

│ │ │

mia-2dimageseries-maximum-intensity-projection

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dimagefullstats	Home	mia-2dimagestats

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dimagestackcmeans.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-2dimagestack-cmeans

mia-2dimagestack-cmeans
Prev	Processing of series of 2D images in a 3D fashion (out-of-core)	Next

mia-2dimagestack-cmeans

Sysnopis:

mia-2dimagestack-cmeans {-i io} {-o string} [ │ │ │ options │ │ │ - ...]

Description:

This program first evaluates a sparse histogram of an input image series, then runs a c-means classification over the histogram and then writes the probability mapping for thr original intensity values

Options:

File-IO

-i, --in-file=(required, input); io: input image(s) to be filtered. For supported file types see Plugin type: 2dimage/io
-o, --out-probmap=(required, output); string: Save probability map to this file

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Parameters

-T, --histogram-thresh=5; float in [0, 50]: Percent of the extrem parts of the histogram to be collapsed into the respective last histogram bin.
-C, --classes=kmeans:nc=3; factory: C-means class initializer. For supported plug-ins see Plugin type: 1d/cmeans

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run the program over images imageXXXX.png with the sparse histogram, threshold the lower 5% bins (if available), run cmeans with three classes on the non-zero pixels.

mia-2dimagestack-cmeans -i image0000.png -o cmeans,txt --histogram-tresh=5 --classes 3

Author(s):

Gert Wollny

Prev	Up	Next
Processing of series of 2D images in a 3D fashion (out-of-core)	Home	mia-2dstack-cmeans-presegment

│ │ │ + ...]

Description:

Options:

File-IO

-i, --in-file=(input, required); io: input image(s) to be filtered. For supported file types see Plugin type: 2dimage/io
-o, --out-probmap=(output, required); string: Save probability map to this file

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Parameters

-T, --histogram-thresh=5; float in [0, 50]: Percent of the extrem parts of the histogram to be collapsed into the respective last histogram bin.
-C, --classes=kmeans:nc=3; factory: C-means class initializer. For supported plug-ins see Plugin type: 1d/cmeans

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run the program over images imageXXXX.png with the sparse histogram, threshold the lower 5% bins (if available), run cmeans with three classes on the non-zero pixels.

mia-2dimagestack-cmeans -i image0000.png -o cmeans,txt --histogram-tresh=5 --classes 3

Author(s):

Gert Wollny

Prev	Up	Next
Processing of series of 2D images in a 3D fashion (out-of-core)	Home	mia-2dstack-cmeans-presegment

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dimagestats.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-2dimagestats

mia-2dimagestats
Prev	Analysis, filtering, combining, and segmentation of 2D images	Next

mia-2dimagestats

Sysnopis:

mia-2dimagestats {-i io} [ │ │ │ options │ │ │ - ...]

Description:

This progranm is used to evaluate some statistics of an image. Output is Mean, Variation, Median, and Median Average Distance of the intensity values. The program allows one to set a lower threshold and to cut off a percentage of the high intensity pixels

Options:

-i, --in-file=(required, input); io: input image to be analyzed. For supported file types see Plugin type: 2dimage/io
-t, --thresh=10; float: intensity thresh to ignore
-g, --high-thresh=0.05; float: upper histogram percentage to ignore
--use-histogram: Use a histogram to accumulate statistics

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the statistics of image input.png. Don't include the upper 1% of intensities in the statistics. The result is written to stdout

mia-2dimagestats -i input.png -g 1

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dimageseries-maximum-intensity-projection	Home	mia-2dlerp

│ │ │ + ...]

Description:

Options:

-i, --in-file=(input, required); io: input image to be analyzed. For supported file types see Plugin type: 2dimage/io
-t, --thresh=10; float: intensity thresh to ignore
-g, --high-thresh=0.05; float: upper histogram percentage to ignore
--use-histogram: Use a histogram to accumulate statistics

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the statistics of image input.png. Don't include the upper 1% of intensities in the statistics. The result is written to stdout

mia-2dimagestats -i input.png -g 1

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dimageseries-maximum-intensity-projection	Home	mia-2dlerp

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dlerp.html │ │ │ @@ -1,7 +1,7 @@ │ │ │ mia-2dlerp

mia-2dlerp
Prev	Analysis, filtering, combining, and segmentation of 2D images	Next

mia-2dlerp

Sysnopis:

mia-2dlerp {-1 io} {-2 io} {-o io} {-p vfloat} [ │ │ │ options │ │ │ - ...]

Description:

Merge two images by pixel-wise linearly combining their intensities.

Options:

-1, --first=(required, input); io: first input image . For supported file types see Plugin type: 2dimage/io
-2, --second=(required, input); io: second input image . For supported file types see Plugin type: 2dimage/io
-o, --out-file=(required, output); io: output vector field. For supported file types see Plugin type: 2dimage/io
-p, --positions=(required); vfloat: image series positions (first, target, second)

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Test

--selftest=(: run a self test of the program

Example:

Combine image inputA.v and inputB.v by using position coordinates 4, 7, and 9. This means the output pixel values will be evaluated according to │ │ │ + ...]

Description:

Merge two images by pixel-wise linearly combining their intensities.

Options:

-1, --first=(input, required); io: first input image . For supported file types see Plugin type: 2dimage/io
-2, --second=(input, required); io: second input image . For supported file types see Plugin type: 2dimage/io
-o, --out-file=(output, required); io: output vector field. For supported file types see Plugin type: 2dimage/io
-p, --positions=(required); vfloat: image series positions (first, target, second)

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Test

--selftest=(: run a self test of the program

Example:

Combine image inputA.v and inputB.v by using position coordinates 4, 7, and 9. This means the output pixel values will be evaluated according to │ │ │ │ │ │ (9-7)/(9-4) * A + (7-4)/(9-4) * B │ │ │ │ │ │ The result image will be written to output.v

mia-2dlerp -1 inputA.v -2 inputB.v -p 4,7,9 -o output.v

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dimagestats	Home	mia-2dmultiimagevar

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dmany2onenonrigid.html │ │ │ @@ -1,9 +1,9 @@ │ │ │ mia-2dmany2one-nonrigid

mia-2dmany2one-nonrigid
Prev	Registration of series of 2D images	Next

mia-2dmany2one-nonrigid

Sysnopis:

mia-2dmany2one-nonrigid {-i string} {-o string} [ │ │ │ options │ │ │ ...] [ │ │ │ │ │ │ Plugin type: 2dimage/fullcost │ │ │ │ │ │ ...]

Description:

This program registers all images of a conscutively numbered set of images to one common user defined reference.

Options:

│ │ │ -File-IO

-i, --in-file=(required, input); string: input perfusion data set
-o, --out-file=(required, output); string: file name for registered images, numbering and pattern are deducted from the input data

│ │ │ +File-IO

-i, --in-file=(input, required); string: input perfusion data set
-o, --out-file=(output, required); string: file name for registered images, numbering and pattern are deducted from the input data

│ │ │ Registration

-O, --optimizer=gsl:opt=gd,step=0.1; stringSTRING: Optimizer used for minimization
-l, --mg-levels=3; ulong: multi-resolution levels
-f, --transForm=spline; factory: transformation type. For supported plug-ins see Plugin type: 2dimage/transform
-r, --ref=-1; int: reference frame (-1 == use image in the middle)
-k, --skip=0; int: skip registration of these images at the beginning of the series

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Register the image series given by images 'inputXXXX.png' to reference image 30. Skip two images at the beginning and using mutual information as cost function, and penalize the transformation by divcurl with weight 5. Store the result in 'registeredXXXX.png'.

mia-2dmany2one-nonrigid   -i input0000.png -o registered%04d.png -k 2 -r 30 image:cost=mi divcurl:weight=5

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dgroundtruthreg	Home	mia-2dmyoica-full

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dmultiforce.html │ │ │ @@ -1,9 +1,9 @@ │ │ │ mia-2dmulti-force

mia-2dmulti-force
Prev	Registration, Comparison, and Transformation of 2D images	Next

mia-2dmulti-force

Sysnopis:

mia-2dmulti-force {-o io} [ │ │ │ options │ │ │ ...] [ │ │ │ │ │ │ Plugin type: 2dimage/fullcost │ │ │ │ │ │ - ...]

Description:

This program evaluates the 2D image cost force norm image of a given cost function set. The input images must be of the same dimensions and gray scale (whatever bit-depth).

Options:

-o, --out-file=(required, output); io: output norm image. For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the force normimage weighted sum of costs SSD and NGF of image1.v and image2.v. and store the result to force.v.

mia-2dmulti-force -o force.v │ │ │ + ...]

Description:

This program evaluates the 2D image cost force norm image of a given cost function set. The input images must be of the same dimensions and gray scale (whatever bit-depth).

Options:

-o, --out-file=(output, required); io: output norm image. For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the force normimage weighted sum of costs SSD and NGF of image1.v and image2.v. and store the result to force.v.

mia-2dmulti-force -o force.v 
│ │ │   image:cost=ssd,src=image1.v,ref=image2.v,weight=0.1
│ │ │   image:cost=ngf,src=image1.v,ref=image2.v,weight=2.0

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dimageregistration	Home	mia-2dmultiimageregistration

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dmultiimageregistration.html │ │ │ @@ -1,9 +1,9 @@ │ │ │ mia-2dmultiimageregistration

mia-2dmultiimageregistration
Prev	Registration, Comparison, and Transformation of 2D images	Next

mia-2dmultiimageregistration

Sysnopis:

mia-2dmultiimageregistration {-o io} [ │ │ │ options │ │ │ ...] [ │ │ │ │ │ │ Plugin type: 2dimage/fullcost │ │ │ │ │ │ - ...]

Description:

This program runs a non-rigid registration based on the given cost criteria and a given transformation model. Other than mia-2dnonrigidreg it doesn't support specific command line parameters to provide the images. Instead the images are specified dirctly when defining the cost function. Hence, image registrations can be executed that optimize the aligmnet of more than one image pair at the same time. Note, however, that all input images must be of the same dimension (in pixels)

Options:

-o, --out-transform=(required, output); io: output transformation. For supported file types see Plugin type: 2dtransform/io
-l, --levels=3; ulong: multi-resolution levels
-O, --optimizer=gsl:opt=gd,step=0.1; factory: Optimizer used for minimization. For supported plug-ins see Plugin type: minimizer/singlecost
-f, --transForm=spline:rate=10,penalty=divcurl; factory: transformation type. For supported plug-ins see Plugin type: 2dimage/transform

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Register image test.v to image ref.v by using a spline transformation with a coefficient rate of 5 and write the registered image to reg.v. Use two multiresolution levels, ssd as image cost function and divcurl weighted by 10.0 as transformation smoothness penalty. The resulting transformation is saved in reg.vf.

mia-2dmultiimageregistration -o reg.vf -l 2 │ │ │ + ...]

Description:

Options:

-o, --out-transform=(output, required); io: output transformation. For supported file types see Plugin type: 2dtransform/io
-l, --levels=3; ulong: multi-resolution levels
-O, --optimizer=gsl:opt=gd,step=0.1; factory: Optimizer used for minimization. For supported plug-ins see Plugin type: minimizer/singlecost
-f, --transForm=spline:rate=10,penalty=divcurl; factory: transformation type. For supported plug-ins see Plugin type: 2dimage/transform

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

mia-2dmultiimageregistration -o reg.vf -l 2
│ │ │   -f spline:rate=3,penalty=divcurl
│ │ │   image:cost=ssd,src=test.v,ref=ref.v

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dmulti-force	Home	mia-2dtransform

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dmultiimageto3d.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-2dmultiimageto3d

mia-2dmultiimageto3d
Prev	Image conversion	Next

mia-2dmultiimageto3d

Sysnopis:

mia-2dmultiimageto3d {-i io} {-o io} [ │ │ │ options │ │ │ - ...]

Description:

This program is used to convert a 2D multi-image file to a 3D image.

Options:

-i, --in-file=(required, input); io: input images. For supported file types see Plugin type: 2dimage/io
-o, --out-file=(required, output); io: output image. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Convert an series of images stored in a 2D image container multiimage2d.v to a 3D image image3d.v.

mia-2dmultiimageto3d -i multiimage2d.v -o image3d.v

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dimageselect	Home	mia-2dto3dimage

│ │ │ + ...]

Description:

This program is used to convert a 2D multi-image file to a 3D image.

Options:

-i, --in-file=(input, required); io: input images. For supported file types see Plugin type: 2dimage/io
-o, --out-file=(output, required); io: output image. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Convert an series of images stored in a 2D image container multiimage2d.v to a 3D image image3d.v.

mia-2dmultiimageto3d -i multiimage2d.v -o image3d.v

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dimageselect	Home	mia-2dto3dimage

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dmultiimagevar.html │ │ │ @@ -1,7 +1,7 @@ │ │ │ mia-2dmultiimagevar

mia-2dmultiimagevar
Prev	Analysis, filtering, combining, and segmentation of 2D images	Next

mia-2dmultiimagevar

Sysnopis:

mia-2dmultiimagevar {-o io} [ │ │ │ options │ │ │ ...] [ │ │ │ │ │ │ Plugin type: 2dimage/io │ │ │ │ │ │ - ...]

Description:

This program evaluates the pixel-wise accumulated intensity variation of a set of image given on the command line. If the input image files contain more then one image all images are used. All images must be of the same size.

Options:

-o, --out-file=(required, output); io: output image . For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the pixel-vise intensity variation of images i1.png, i2.png, i3.png, and i4.png and store the result to var.v.

mia-2dmultiimagevar -o var.v i1.png i2.png i3.png i4.png

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dlerp	Home	mia-2dsegment-ahmed

│ │ │ + ...]

Description:

Options:

-o, --out-file=(output, required); io: output image . For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the pixel-vise intensity variation of images i1.png, i2.png, i3.png, and i4.png and store the result to var.v.

mia-2dmultiimagevar -o var.v i1.png i2.png i3.png i4.png

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dlerp	Home	mia-2dsegment-ahmed

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dmyocardica.html │ │ │ @@ -1,4 +1,4 @@ │ │ │ mia-2dmyocard-ica

mia-2dmyocard-ica
Prev	Tools for Myocardial Perfusion Analysis	Next

mia-2dmyocard-ica

Sysnopis:

mia-2dmyocard-ica {-i io} [ │ │ │ options │ │ │ ...]

Description:

This program is used to run a ICA on a series of myocardial perfusion images to create sythetic references that can be used for motion correction by image registration. If the aim is to run a full motion compensation then it is better to create a segmentation set and use mia-2dmyoica-nonrigid. If the input data is given by means of a segmentation set, then on can also use mia-2dmyocard-icaseries. │ │ │ -This program is essentially used to test different options on how to run the ICA forreference image creation.

Options:

-i, --in-base=(required, input); io: input file name ofolloing pattern nameXXXX.ext X=numbers. For supported file types see Plugin type: 2dimage/io
--coefs=STRING: output mixing coefficients to this file
-o, --out-base=(output); string: output file name base
-t, --type=exr; set: output file type Supported values are:(-, @, BMP, DCM, EXR, JPEG, JPG, PNG, RAW, TIF, TIFF, V, VISTA, bmp, dcm, exr, jpeg, jpg, png, raw, tif, tiff, v, vista, )
-k, --skip=2; ulong: skip images at beginning of series
-e, --end=60; ulong: last image in series
-C, --components=0; ulong: nr. of components, 0=estimate automatically
-m, --strip-mean: strip mean image from series
-f, --save-features=STRING: save feature image
-p, --strip-periodic: strip only periodic component
--fastica=internal; factory: FastICA implementationto be used. For supported plug-ins see Plugin type: fastica/implementation
-x, --max-ica-iterations=0; int: max ICA solver iterations
-n, --ica-normalize: ica_normalize feature images
--all-features=STRING: save all feature images to
-L, --LV-crop-amp=0; float: LV crop mask amplification, 0.0 = don't crop

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the synthetic references from images imageXXXX.exr and save them to refXXXX.exr by using five independend components, mean stripping, normalizing, and skipping 2 images.

mia-2dmyocard-ica -i imageXXXX.exr -o ref -k 2 -C 5 -m -n

Author(s):

Gert Wollny

Prev	Up	Next
Tools for Myocardial Perfusion Analysis	Home	mia-2dmyocard-icaseries

│ │ │ +This program is essentially used to test different options on how to run the ICA forreference image creation.

Options:

-i, --in-base=(input, required); io: input file name ofolloing pattern nameXXXX.ext X=numbers. For supported file types see Plugin type: 2dimage/io
--coefs=STRING: output mixing coefficients to this file
-o, --out-base=(output); string: output file name base
-t, --type=exr; set: output file type Supported values are:(-, @, BMP, DCM, EXR, JPEG, JPG, PNG, RAW, TIF, TIFF, V, VISTA, bmp, dcm, exr, jpeg, jpg, png, raw, tif, tiff, v, vista, )
-k, --skip=2; ulong: skip images at beginning of series
-e, --end=60; ulong: last image in series
-C, --components=0; ulong: nr. of components, 0=estimate automatically
-m, --strip-mean: strip mean image from series
-f, --save-features=STRING: save feature image
-p, --strip-periodic: strip only periodic component
--fastica=internal; factory: FastICA implementationto be used. For supported plug-ins see Plugin type: fastica/implementation
-x, --max-ica-iterations=0; int: max ICA solver iterations
-n, --ica-normalize: ica_normalize feature images
--all-features=STRING: save all feature images to
-L, --LV-crop-amp=0; float: LV crop mask amplification, 0.0 = don't crop

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the synthetic references from images imageXXXX.exr and save them to refXXXX.exr by using five independend components, mean stripping, normalizing, and skipping 2 images.

mia-2dmyocard-ica -i imageXXXX.exr -o ref -k 2 -C 5 -m -n

Author(s):

Gert Wollny

Prev	Up	Next
Tools for Myocardial Perfusion Analysis	Home	mia-2dmyocard-icaseries

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dmyocardicaseries.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-2dmyocard-icaseries

mia-2dmyocard-icaseries
Prev	Tools for Myocardial Perfusion Analysis	Next

mia-2dmyocard-icaseries

Sysnopis:

mia-2dmyocard-icaseries {-i string} [ │ │ │ options │ │ │ - ...]

Description:

This program is used to run a ICA on a series of myocardial perfusion images given in a segmentation set in order to create sythetic references that can be used for motion correction by image registration. If the aim is to run a full motion compensation then it is better run mia-2dmyoica-nonrigid, since this program is essentially the same without the registration bits.

Options:

File-IO

-i, --in-file=(required, input); string: input perfusion data set
-r, --references=(output); string: File name base for the reference images. Image type and numbering scheme are taken from the input images.
-c, --save-cropped=(output); string: save cropped set of the original set to this file, the image files will use the stem of the name as file name base
--save-feature=(output); string: save the features images resulting from the ICA and some intermediate images used for the RV-LV segmentation with the given file name base to PNG files. Also save the coefficients of the initial best and the final IC mixing matrix.

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

ICA

--fastica=internal; factory

FastICA implementationto be used. For supported plug-ins see Plugin type: fastica/implementation

-C, --components=0; ulong

ICA components 0 = automatic estimation

--normalize

normalized ICs

--no-meanstrip

don't strip the mean from the mixing curves

-s, --segscale=1.4; float

segment and scale the crop box around the LV (0=no segmentation)

-k, --skip=0; ulong

skip images at the beginning of the series as they are of other modalities

-m, --max-ica-iter=400; ulong

maximum number of iterations in ICA

-E, --segmethod=features; dict

Segmentation method

delta-feature:	difference of the feature images
delta-peak:	difference of the peak enhancement images
features:	feature images

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the synthetic references from set segment.set and save them to refXXXX.??? by using five independend components, and skipping 2 images. Per default a bounding box around the LV will be segmented and scaled by 1.4 and the cropped images will be saved to cropXXXX.??? and a segmentation set cropped.set is created. The image file type ??? is deducted from the input images in segment.set.

mia-2dmyocard-icaseries -i segment.set -r ref -o ref -k 2 -C 5

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dmyocard-ica	Home	mia-2dmyoseries-compdice

│ │ │ + ...]

Description:

Options:

File-IO

-i, --in-file=(input, required); string: input perfusion data set
-r, --references=(output); string: File name base for the reference images. Image type and numbering scheme are taken from the input images.
-c, --save-cropped=(output); string: save cropped set of the original set to this file, the image files will use the stem of the name as file name base
--save-feature=(output); string: save the features images resulting from the ICA and some intermediate images used for the RV-LV segmentation with the given file name base to PNG files. Also save the coefficients of the initial best and the final IC mixing matrix.

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

ICA

--fastica=internal; factory

FastICA implementationto be used. For supported plug-ins see Plugin type: fastica/implementation

-C, --components=0; ulong

ICA components 0 = automatic estimation

--normalize

normalized ICs

--no-meanstrip

don't strip the mean from the mixing curves

-s, --segscale=1.4; float

segment and scale the crop box around the LV (0=no segmentation)

-k, --skip=0; ulong

skip images at the beginning of the series as they are of other modalities

-m, --max-ica-iter=400; ulong

maximum number of iterations in ICA

-E, --segmethod=features; dict

Segmentation method

delta-feature:	difference of the feature images
delta-peak:	difference of the peak enhancement images
features:	feature images

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

mia-2dmyocard-icaseries -i segment.set -r ref -o ref -k 2 -C 5

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dmyocard-ica	Home	mia-2dmyoseries-compdice

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dmyocardsegment.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-2dmyocard-segment

mia-2dmyocard-segment
Prev	Work in progress	Next

mia-2dmyocard-segment

Sysnopis:

mia-2dmyocard-segment {-i string} {-o io} [ │ │ │ options │ │ │ - ...]

Description:

This program is work in progress

Options:

File-IO

-i, --in-file=(required, input); string: input perfusion data set
-o, --out-file=(required, output); io: output myocardial mask. For supported file types see Plugin type: 2dimage/io
-f, --save-features=(output); string: save ICA features to files with this name base

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

ICA

--fastica=internal; factory: FastICA implementationto be used. For supported plug-ins see Plugin type: fastica/implementation
-C, --components=0; ulong: ICA components 0 = automatic estimation testing 4 and 5
--normalize: normalized ICs
--no-meanstrip: don't strip the mean from the mixing curves
-k, --skip=2; ulong: skip images at the beginning of the series as they are of other modalities
-m, --max-ica-iter=400; ulong: maximum number of iterations in ICA

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Example

mia-2dmyocard-segment Example

Author(s):

Gert Wollny

Prev	Up	Next
Work in progress	Home	Chapter 3. Plugin Reference

│ │ │ + ...]

Description:

This program is work in progress

Options:

File-IO

-i, --in-file=(input, required); string: input perfusion data set
-o, --out-file=(output, required); io: output myocardial mask. For supported file types see Plugin type: 2dimage/io
-f, --save-features=(output); string: save ICA features to files with this name base

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

ICA

--fastica=internal; factory: FastICA implementationto be used. For supported plug-ins see Plugin type: fastica/implementation
-C, --components=0; ulong: ICA components 0 = automatic estimation testing 4 and 5
--normalize: normalized ICs
--no-meanstrip: don't strip the mean from the mixing curves
-k, --skip=2; ulong: skip images at the beginning of the series as they are of other modalities
-m, --max-ica-iter=400; ulong: maximum number of iterations in ICA

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Example

mia-2dmyocard-segment Example

Author(s):

Gert Wollny

Prev	Up	Next
Work in progress	Home	Chapter 3. Plugin Reference

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dmyoicafull.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-2dmyoica-full

mia-2dmyoica-full
Prev	Registration of series of 2D images	Next

mia-2dmyoica-full

Sysnopis:

mia-2dmyoica-full {-i string} {-o string} [ │ │ │ options │ │ │ - ...]

Description:

This program implements the 2D version of the motion compensation algorithm described in

Wollny G, Kellman P, Santos A, Ledesma-Carbayo M-J, "Automatic Motion Compensation of Free Breathing acquired Myocardial Perfusion Data by using Independent Component Analysis", Medical Image Analysis, 2012.

The software may first run a linear registration and then a non-linear registration or just one of the two.This version of the program can run all registrations in parallel.

Options:

File-IO

-i, --in-file=(required, input); string: input perfusion data set
-o, --out-file=(required, output); string: output perfusion data set
-r, --registered=STRING: File name base for the registered images. Image type and numbering scheme are taken from the input images as given in the input data set.
--save-cropped=(output); string: save cropped set to this file, the image files will use the stem of the name as file name base
--save-feature=(output); string: save segmentation feature images and initial ICA mixing matrix
--save-refs=(output); string: for each registration pass save the reference images to files with the given name base
--save-regs=(output); string: for each registration pass save intermediate registered images

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

ICA

--fastica=internal; factory

FastICA implementationto be used. For supported plug-ins see Plugin type: fastica/implementation

-C, --components=0; ulong

ICA components 0 = automatic estimation

--normalize

normalized ICs

--no-meanstrip

don't strip the mean from the mixing curves

-s, --segscale=0; float

segment and scale the crop box around the LV (0=no segmentation)

-k, --skip=0; ulong

skip images at the beginning of the series e.g. because as they are of other modalities

-m, --max-ica-iter=400; ulong

maximum number of iterations in ICA

-E, --segmethod=features; dict

Segmentation method

delta-feature:	difference of the feature images
delta-peak:	difference of the peak enhancement images
features:	feature images

-b, --min-breathing-frequency=-1; float

minimal mean frequency a mixing curve can have to be considered to stem from brething. A healthy rest breating rate is 12 per minute. A negative value disables the test. A value 0.0 forces the series to be identified as acquired with initial breath hold.

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Registration

-L, --linear-optimizer=gsl:opt=simplex,step=1.0; factory: Optimizer used for minimization of the linear registration The string value will be used to construct a plug-in.. For supported plug-ins see Plugin type: minimizer/singlecost
--linear-transform=affine; factory: linear transform to be used The string value will be used to construct a plug-in.. For supported plug-ins see Plugin type: 2dimage/transform
-O, --non-linear-optimizer=gsl:opt=gd,step=0.1; factory: Optimizer used for minimization in the non-linear registration. The string value will be used to construct a plug-in.. For supported plug-ins see Plugin type: minimizer/singlecost
-a, --start-c-rate=16; double: start coefficinet rate in spines, gets divided by --c-rate-divider with every pass.
--c-rate-divider=2; double: Cofficient rate divider for each pass.
-d, --start-divcurl=10000; double: Start divcurl weight, gets divided by --divcurl-divider with every pass.
--divcurl-divider=2; double: Divcurl weight scaling with each new pass.
-R, --reference=-1; int: Global reference all image should be aligned to. If set to a non-negative value, the images will be aligned to this references, and the cropped output image date will be injected into the original images. Leave at -1 if you don't care. In this case all images with be registered to a mean position of the movement
-w, --imagecost=image:weight=1,cost=ssd; factory: image cost, do not specify the src and ref parameters, these will be set by the program. The string value will be used to construct a plug-in.. For supported plug-ins see Plugin type: 2dimage/fullcost
-l, --mg-levels=3; ulong: multi-resolution levels
-p, --linear-passes=3; ulong: linear registration passes (0 to disable)
-P, --nonlinear-passes=3; ulong: non-linear registration passes (0 to disable)

Example:

Register the perfusion series given in 'segment.set' by using automatic ICA estimation. Skip two images at the beginning and otherwiese use the default parameters. Store the result in 'registered.set'.

mia-2dmyoica-full   -i segment.set -o registered.set -k 2

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dmany2one-nonrigid	Home	mia-2dmyoica-nonrigid

│ │ │ + ...]

Description:

This program implements the 2D version of the motion compensation algorithm described in

The software may first run a linear registration and then a non-linear registration or just one of the two.This version of the program can run all registrations in parallel.

Options:

File-IO

-i, --in-file=(input, required); string: input perfusion data set
-o, --out-file=(output, required); string: output perfusion data set
-r, --registered=STRING: File name base for the registered images. Image type and numbering scheme are taken from the input images as given in the input data set.
--save-cropped=(output); string: save cropped set to this file, the image files will use the stem of the name as file name base
--save-feature=(output); string: save segmentation feature images and initial ICA mixing matrix
--save-refs=(output); string: for each registration pass save the reference images to files with the given name base
--save-regs=(output); string: for each registration pass save intermediate registered images

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

ICA

--fastica=internal; factory

FastICA implementationto be used. For supported plug-ins see Plugin type: fastica/implementation

-C, --components=0; ulong

ICA components 0 = automatic estimation

--normalize

normalized ICs

--no-meanstrip

don't strip the mean from the mixing curves

-s, --segscale=0; float

segment and scale the crop box around the LV (0=no segmentation)

-k, --skip=0; ulong

skip images at the beginning of the series e.g. because as they are of other modalities

-m, --max-ica-iter=400; ulong

maximum number of iterations in ICA

-E, --segmethod=features; dict

Segmentation method

delta-feature:	difference of the feature images
delta-peak:	difference of the peak enhancement images
features:	feature images

-b, --min-breathing-frequency=-1; float

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Registration

-L, --linear-optimizer=gsl:opt=simplex,step=1.0; factory: Optimizer used for minimization of the linear registration The string value will be used to construct a plug-in.. For supported plug-ins see Plugin type: minimizer/singlecost
--linear-transform=affine; factory: linear transform to be used The string value will be used to construct a plug-in.. For supported plug-ins see Plugin type: 2dimage/transform
-O, --non-linear-optimizer=gsl:opt=gd,step=0.1; factory: Optimizer used for minimization in the non-linear registration. The string value will be used to construct a plug-in.. For supported plug-ins see Plugin type: minimizer/singlecost
-a, --start-c-rate=16; double: start coefficinet rate in spines, gets divided by --c-rate-divider with every pass.
--c-rate-divider=2; double: Cofficient rate divider for each pass.
-d, --start-divcurl=10000; double: Start divcurl weight, gets divided by --divcurl-divider with every pass.
--divcurl-divider=2; double: Divcurl weight scaling with each new pass.
-R, --reference=-1; int: Global reference all image should be aligned to. If set to a non-negative value, the images will be aligned to this references, and the cropped output image date will be injected into the original images. Leave at -1 if you don't care. In this case all images with be registered to a mean position of the movement
-w, --imagecost=image:weight=1,cost=ssd; factory: image cost, do not specify the src and ref parameters, these will be set by the program. The string value will be used to construct a plug-in.. For supported plug-ins see Plugin type: 2dimage/fullcost
-l, --mg-levels=3; ulong: multi-resolution levels
-p, --linear-passes=3; ulong: linear registration passes (0 to disable)
-P, --nonlinear-passes=3; ulong: non-linear registration passes (0 to disable)

Example:

mia-2dmyoica-full   -i segment.set -o registered.set -k 2

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dmany2one-nonrigid	Home	mia-2dmyoica-nonrigid

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dmyoicanonrigid.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-2dmyoica-nonrigid

mia-2dmyoica-nonrigid
Prev	Registration of series of 2D images	Next

mia-2dmyoica-nonrigid

Sysnopis:

mia-2dmyoica-nonrigid {-i string} {-o string} [ │ │ │ options │ │ │ - ...]

Description:

This program implements the motion compensation algorithm described in

Options:

File-IO

-i, --in-file=(required, input); string: input perfusion data set
-o, --out-file=(required, output); string: output perfusion data set
-r, --registered=reg; stringSTRING: file name base for registered fiels
--save-cropped=STRING: save cropped set to this file
--save-feature=STRING: save the features images resulting from the ICA and some intermediate images used for the RV-LV segmentation with the given file name base to PNG files. Also save the coefficients of the initial best and the final IC mixing matrix.
--save-refs=STRING: save synthetic reference images
--save-regs=STRING: save intermediate registered images

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

ICA

--fastica=internal; factory

FastICA implementationto be used. For supported plug-ins see Plugin type: fastica/implementation

-C, --components=0; ulong

ICA components 0 = automatic estimation

--normalize

normalized ICs

--no-meanstrip

don't strip the mean from the mixing curves

-s, --segscale=0; float

segment and scale the crop box around the LV (0=no segmentation)

-k, --skip=0; ulong

skip images at the beginning of the series e.g. because as they are of other modalities

-m, --max-ica-iter=400; ulong

maximum number of iterations in ICA

-E, --segmethod=features; dict

Segmentation method

delta-feature:	difference of the feature images
delta-peak:	difference of the peak enhancement images
features:	feature images

-b, --min-breathing-frequency=-1; float

minimal mean frequency a mixing curve can have to be considered to stem from brething. A healthy rest breating rate is 12 per minute. A negative value disables the test.

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Registration

-O, --optimizer=gsl:opt=gd,step=0.1; factory: Optimizer used for minimization. For supported plug-ins see Plugin type: minimizer/singlecost
-R, --refiner=: optimizer used for refinement after the main optimizer was called. For supported plug-ins see Plugin type: minimizer/singlecost
-a, --start-c-rate=16; double: start coefficinet rate in spines, gets divided by --c-rate-divider with every pass
--c-rate-divider=2; double: cofficient rate divider for each pass
-d, --start-divcurl=10; double: start divcurl weight, gets divided by --divcurl-divider with every pass
--divcurl-divider=2; double: divcurl weight scaling with each new pass
-w, --imagecost=image:weight=1,cost=ssd; factory: image cost. For supported plug-ins see Plugin type: 2dimage/fullcost
-l, --mg-levels=3; ulong: multi-resolution levels
-P, --passes=5; ulong: registration passes

Example:

mia-2dmyoica-nonrigid   -i segment.set -o registered.set -k 2

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dmyoica-full	Home	mia-2dmyoica-nonrigid-parallel

│ │ │ + ...]

Description:

This program implements the motion compensation algorithm described in

Options:

File-IO

-i, --in-file=(input, required); string: input perfusion data set
-o, --out-file=(output, required); string: output perfusion data set
-r, --registered=reg; stringSTRING: file name base for registered fiels
--save-cropped=STRING: save cropped set to this file
--save-feature=STRING: save the features images resulting from the ICA and some intermediate images used for the RV-LV segmentation with the given file name base to PNG files. Also save the coefficients of the initial best and the final IC mixing matrix.
--save-refs=STRING: save synthetic reference images
--save-regs=STRING: save intermediate registered images

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

ICA

--fastica=internal; factory

FastICA implementationto be used. For supported plug-ins see Plugin type: fastica/implementation

-C, --components=0; ulong

ICA components 0 = automatic estimation

--normalize

normalized ICs

--no-meanstrip

don't strip the mean from the mixing curves

-s, --segscale=0; float

segment and scale the crop box around the LV (0=no segmentation)

-k, --skip=0; ulong

skip images at the beginning of the series e.g. because as they are of other modalities

-m, --max-ica-iter=400; ulong

maximum number of iterations in ICA

-E, --segmethod=features; dict

Segmentation method

delta-feature:	difference of the feature images
delta-peak:	difference of the peak enhancement images
features:	feature images

-b, --min-breathing-frequency=-1; float

minimal mean frequency a mixing curve can have to be considered to stem from brething. A healthy rest breating rate is 12 per minute. A negative value disables the test.

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Registration

-O, --optimizer=gsl:opt=gd,step=0.1; factory: Optimizer used for minimization. For supported plug-ins see Plugin type: minimizer/singlecost
-R, --refiner=: optimizer used for refinement after the main optimizer was called. For supported plug-ins see Plugin type: minimizer/singlecost
-a, --start-c-rate=16; double: start coefficinet rate in spines, gets divided by --c-rate-divider with every pass
--c-rate-divider=2; double: cofficient rate divider for each pass
-d, --start-divcurl=10; double: start divcurl weight, gets divided by --divcurl-divider with every pass
--divcurl-divider=2; double: divcurl weight scaling with each new pass
-w, --imagecost=image:weight=1,cost=ssd; factory: image cost. For supported plug-ins see Plugin type: 2dimage/fullcost
-l, --mg-levels=3; ulong: multi-resolution levels
-P, --passes=5; ulong: registration passes

Example:

mia-2dmyoica-nonrigid   -i segment.set -o registered.set -k 2

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dmyoica-full	Home	mia-2dmyoica-nonrigid-parallel

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dmyoicanonrigid2.html │ │ │ @@ -1,7 +1,7 @@ │ │ │ mia-2dmyoica-nonrigid2

mia-2dmyoica-nonrigid2
Prev	Registration of series of 2D images	Next

mia-2dmyoica-nonrigid2

Sysnopis:

mia-2dmyoica-nonrigid2 {-i string} {-o string} [ │ │ │ options │ │ │ ...]

Description:

This program runs the non-rigid registration of an perfusion image series.In each pass, first an ICA analysis is run to estimate and eliminate the periodic movement and create reference images with intensities similar to the corresponding original image. Then non-rigid registration is run using the an "ssd + divcurl" cost model. The B-spline c-rate and the divcurl cost weight are changed in each pass according to given parameters.In the first pass a bounding box around the LV myocardium may be extractedto speed up computation │ │ │ Special note to this implemnentation: the registration is always run from the original images to avoid the accumulation of interpolation errors.

Options:

│ │ │ -File-IO

-i, --in-file=(required, input); string: input perfusion data set
-o, --out-file=(required, output); string: output perfusion data set
-r, --registered=reg; stringSTRING: file name base for registered fiels
--save-cropped=STRING: save cropped set to this file
--save-feature=STRING: save segmentation feature images and initial ICA mixing matrix

│ │ │ +File-IO

-i, --in-file=(input, required); string: input perfusion data set
-o, --out-file=(output, required); string: output perfusion data set
-r, --registered=reg; stringSTRING: file name base for registered fiels
--save-cropped=STRING: save cropped set to this file
--save-feature=STRING: save segmentation feature images and initial ICA mixing matrix

│ │ │ ICA

--fastica=internal; factory

FastICA implementationto be used. For supported plug-ins see Plugin type: fastica/implementation

-C, --components=0; ulong

ICA components 0 = automatic estimation

--normalize

don't normalized ICs

--no-meanstrip

don't strip the mean from the mixing curves

-s, --segscale=0; float

segment and scale the crop box around the LV (0=no segmentation)

-k, --skip=0; ulong

skip images at the beginning of the series e.g. because as they are of other modalities

-m, --max-ica-iter=400; ulong

maximum number of iterations in ICA

-E, --segmethod=features; dict

Segmentation method

delta-feature:	difference of the feature images
delta-peak:	difference of the peak enhancement images
features:	feature images

│ │ │ Registration

-O, --optimizer=gsl:opt=gd,step=0.1; factory: Optimizer used for minimization. For supported plug-ins see Plugin type: minimizer/singlecost
-a, --start-c-rate=32; double: start coefficinet rate in spines, gets divided by --c-rate-divider with every pass
--c-rate-divider=4; double: cofficient rate divider for each pass
-d, --start-divcurl=20; double: start divcurl weight, gets divided by --divcurl-divider with every pass
--divcurl-divider=4; double: divcurl weight scaling with each new pass
-w, --imageweight=1; double: image cost weight
-p, --interpolator=bspline:d=3; factory: image interpolator kernel. For supported plug-ins see Plugin type: 1d/splinekernel
-l, --mg-levels=3; ulong: multi-resolution levels
-P, --passes=3; ulong: registration passes

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

mia-2dmyoica-nonrigid2   -i segment.set -o registered.set -k 2

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dmyoica-nonrigid-parallel	Home	mia-2dmyoicapgt

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dmyoicanonrigidparallel.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-2dmyoica-nonrigid-parallel

mia-2dmyoica-nonrigid-parallel
Prev	Registration of series of 2D images	Next

mia-2dmyoica-nonrigid-parallel

Sysnopis:

mia-2dmyoica-nonrigid-parallel {-i string} {-o string} [ │ │ │ options │ │ │ - ...]

Description:

This program implements the 2D version of the motion compensation algorithm described in

This version of the program runs all registrations in parallel.

Options:

File-IO

-i, --in-file=(required, input); string: input perfusion data set
-o, --out-file=(required, output); string: output perfusion data set
-r, --registered=reg; stringSTRING: File name base for the registered images. Image type and numbering scheme are taken from the input images as given in the input data set.
--save-cropped=(output); string: save cropped set to this file, the image files will use the stem of the name as file name base
--save-feature=(output); string: save segmentation feature images and initial ICA mixing matrix
--save-refs=(output); string: for each registration pass save the reference images to files with the given name base
--save-regs=(output); string: for each registration pass save intermediate registered images

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

ICA

--fastica=internal; factory

FastICA implementationto be used. For supported plug-ins see Plugin type: fastica/implementation

-C, --components=0; ulong

ICA components 0 = automatic estimation

--normalize

normalized ICs

--no-meanstrip

don't strip the mean from the mixing curves

-s, --segscale=0; float

segment and scale the crop box around the LV (0=no segmentation)

-k, --skip=0; ulong

skip images at the beginning of the series e.g. because as they are of other modalities

-m, --max-ica-iter=400; ulong

maximum number of iterations in ICA

-E, --segmethod=features; dict

Segmentation method

delta-feature:	difference of the feature images
delta-peak:	difference of the peak enhancement images
features:	feature images

-b, --min-breathing-frequency=-1; float

minimal mean frequency a mixing curve can have to be considered to stem from brething. A healthy rest breating rate is 12 per minute. A negative value disables the test.

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Registration

-O, --optimizer=gsl:opt=gd,step=0.1; factory: Optimizer used for minimization. The string value will be used to construct a plug-in.. For supported plug-ins see Plugin type: minimizer/singlecost
-a, --start-c-rate=16; double: start coefficinet rate in spines, gets divided by --c-rate-divider with every pass.
--c-rate-divider=2; double: Cofficient rate divider for each pass.
-d, --start-divcurl=10000; double: Start divcurl weight, gets divided by --divcurl-divider with every pass.
--divcurl-divider=2; double: Divcurl weight scaling with each new pass.
-w, --imagecost=image:weight=1,cost=ssd; factory: image cost, do not specify the src and ref parameters, these will be set by the program. The string value will be used to construct a plug-in.. For supported plug-ins see Plugin type: 2dimage/fullcost
-l, --mg-levels=3; ulong: multi-resolution levels
-P, --passes=3; ulong: registration passes

Example:

mia-2dmyoica-nonrigid-parallel   -i segment.set -o registered.set -k 2

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dmyoica-nonrigid	Home	mia-2dmyoica-nonrigid2

│ │ │ + ...]

Description:

This program implements the 2D version of the motion compensation algorithm described in

This version of the program runs all registrations in parallel.

Options:

File-IO

-i, --in-file=(input, required); string: input perfusion data set
-o, --out-file=(output, required); string: output perfusion data set
-r, --registered=reg; stringSTRING: File name base for the registered images. Image type and numbering scheme are taken from the input images as given in the input data set.
--save-cropped=(output); string: save cropped set to this file, the image files will use the stem of the name as file name base
--save-feature=(output); string: save segmentation feature images and initial ICA mixing matrix
--save-refs=(output); string: for each registration pass save the reference images to files with the given name base
--save-regs=(output); string: for each registration pass save intermediate registered images

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

ICA

--fastica=internal; factory

FastICA implementationto be used. For supported plug-ins see Plugin type: fastica/implementation

-C, --components=0; ulong

ICA components 0 = automatic estimation

--normalize

normalized ICs

--no-meanstrip

don't strip the mean from the mixing curves

-s, --segscale=0; float

segment and scale the crop box around the LV (0=no segmentation)

-k, --skip=0; ulong

skip images at the beginning of the series e.g. because as they are of other modalities

-m, --max-ica-iter=400; ulong

maximum number of iterations in ICA

-E, --segmethod=features; dict

Segmentation method

delta-feature:	difference of the feature images
delta-peak:	difference of the peak enhancement images
features:	feature images

-b, --min-breathing-frequency=-1; float

minimal mean frequency a mixing curve can have to be considered to stem from brething. A healthy rest breating rate is 12 per minute. A negative value disables the test.

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Registration

-O, --optimizer=gsl:opt=gd,step=0.1; factory: Optimizer used for minimization. The string value will be used to construct a plug-in.. For supported plug-ins see Plugin type: minimizer/singlecost
-a, --start-c-rate=16; double: start coefficinet rate in spines, gets divided by --c-rate-divider with every pass.
--c-rate-divider=2; double: Cofficient rate divider for each pass.
-d, --start-divcurl=10000; double: Start divcurl weight, gets divided by --divcurl-divider with every pass.
--divcurl-divider=2; double: Divcurl weight scaling with each new pass.
-w, --imagecost=image:weight=1,cost=ssd; factory: image cost, do not specify the src and ref parameters, these will be set by the program. The string value will be used to construct a plug-in.. For supported plug-ins see Plugin type: 2dimage/fullcost
-l, --mg-levels=3; ulong: multi-resolution levels
-P, --passes=3; ulong: registration passes

Example:

mia-2dmyoica-nonrigid-parallel   -i segment.set -o registered.set -k 2

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dmyoica-nonrigid	Home	mia-2dmyoica-nonrigid2

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dmyoicapgt.html │ │ │ @@ -1,4 +1,4 @@ │ │ │ mia-2dmyoicapgt

mia-2dmyoicapgt
Prev	Registration of series of 2D images	Next

mia-2dmyoicapgt

Sysnopis:

mia-2dmyoicapgt {-i string} {-o string} [ │ │ │ options │ │ │ ...]

Description:

This program implements a two passs motion compensation algorithm. First a linear registration is run based on a variation of

Gupta et~al. "Fully automatic registration and segmentation of first-pass myocardial perfusion MR image sequences", Academic Radiology 17, 1375-1385

as described in

followed by a non-linear registration based

Chao Li and Ying Sun, "Nonrigid Registration of Myocardial Perfusion MRI Using Pseudo Ground Truth", In Proc. Medical Image Computing and Computer-Assisted Intervention MICCAI 2009, 165-172, 2009.

Note that for this nonlinear motion correction a preceding linear registration step is usually required. This version of the program may run all registrations in parallel.

Options:

│ │ │ -Pseudo Ground Thruth estimation

-A, --alpha=0.1; double: spacial neighborhood penalty weight
-B, --beta=4; double: temporal second derivative penalty weight
-T, --rho-thresh=0.85; double: correlation threshold for neighborhood analysis

File-IO

-i, --in-file=(required, input); string: input perfusion data set
-o, --out-file=(required, output); string: output perfusion data set
-r, --registered=STRING: File name base for the registered images. Image type and numbering scheme are taken from the input images as given in the input data set.
--save-cropped=(output); string: save cropped set to this file, the image files will use the stem of the name as file name base
--save-feature=(output); string: save segmentation feature images and initial ICA mixing matrix
--save-refs=(output); string: for each registration pass save the reference images to files with the given name base
--save-regs=(output); string: for each registration pass save intermediate registered images

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

ICA

--fastica=internal; factory

FastICA implementationto be used. For supported plug-ins see Plugin type: fastica/implementation

-C, --components=0; ulong

ICA components 0 = automatic estimation

--normalize

normalized ICs

--no-meanstrip

don't strip the mean from the mixing curves

-s, --segscale=0; float

segment and scale the crop box around the LV (0=no segmentation)

-k, --skip=0; ulong

skip images at the beginning of the series e.g. because as they are of other modalities

-m, --max-ica-iter=400; ulong

maximum number of iterations in ICA

-E, --segmethod=features; dict

Segmentation method

delta-feature:	difference of the feature images
delta-peak:	difference of the peak enhancement images
features:	feature images

-b, --min-breathing-frequency=-1; float

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Registration

-L, --linear-optimizer=gsl:opt=simplex,step=1.0; factory: Optimizer used for minimization of the linear registration The string value will be used to construct a plug-in.. For supported plug-ins see Plugin type: minimizer/singlecost
--linear-transform=affine; factory: linear transform to be used The string value will be used to construct a plug-in.. For supported plug-ins see Plugin type: 2dimage/transform
-O, --non-linear-optimizer=gsl:opt=gd,step=0.1; factory: Optimizer used for minimization in the non-linear registration. The string value will be used to construct a plug-in.. For supported plug-ins see Plugin type: minimizer/singlecost
-a, --start-c-rate=16; double: start coefficinet rate in spines, gets divided by --c-rate-divider with every pass.
--c-rate-divider=2; double: Cofficient rate divider for each pass.
-d, --start-divcurl=10000; double: Start divcurl weight, gets divided by --divcurl-divider with every pass.
--divcurl-divider=2; double: Divcurl weight scaling with each new pass.
-R, --reference=-1; int: Global reference all image should be aligned to. If set to a non-negative value, the images will be aligned to this references, and the cropped output image date will be injected into the original images. Leave at -1 if you don't care. In this case all images with be registered to a mean position of the movement
-w, --imagecost=image:weight=1,cost=ssd; factory: image cost, do not specify the src and ref parameters, these will be set by the program. The string value will be used to construct a plug-in.. For supported plug-ins see Plugin type: 2dimage/fullcost
-l, --mg-levels=3; ulong: multi-resolution levels
-p, --linear-passes=3; ulong: linear registration passes (0 to disable)
-P, --nonlinear-passes=3; ulong: non-linear registration passes (0 to disable)

Example:

Register the perfusion series given in 'segment.set' by first using automatic ICA estimation to run the linear registration and then the PGT registration. Skip two images at the beginning and otherwiese use the default parameters. Store the result in 'registered.set'.

mia-2dmyoicapgt   -i segment.set -o registered.set -k 2

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dmyoica-nonrigid2	Home	mia-2dmyomilles

│ │ │ +Pseudo Ground Thruth estimation

-A, --alpha=0.1; double: spacial neighborhood penalty weight
-B, --beta=4; double: temporal second derivative penalty weight
-T, --rho-thresh=0.85; double: correlation threshold for neighborhood analysis

File-IO

-i, --in-file=(input, required); string: input perfusion data set
-o, --out-file=(output, required); string: output perfusion data set
-r, --registered=STRING: File name base for the registered images. Image type and numbering scheme are taken from the input images as given in the input data set.
--save-cropped=(output); string: save cropped set to this file, the image files will use the stem of the name as file name base
--save-feature=(output); string: save segmentation feature images and initial ICA mixing matrix
--save-refs=(output); string: for each registration pass save the reference images to files with the given name base
--save-regs=(output); string: for each registration pass save intermediate registered images

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

ICA

--fastica=internal; factory

FastICA implementationto be used. For supported plug-ins see Plugin type: fastica/implementation

-C, --components=0; ulong

ICA components 0 = automatic estimation

--normalize

normalized ICs

--no-meanstrip

don't strip the mean from the mixing curves

-s, --segscale=0; float

segment and scale the crop box around the LV (0=no segmentation)

-k, --skip=0; ulong

skip images at the beginning of the series e.g. because as they are of other modalities

-m, --max-ica-iter=400; ulong

maximum number of iterations in ICA

-E, --segmethod=features; dict

Segmentation method

delta-feature:	difference of the feature images
delta-peak:	difference of the peak enhancement images
features:	feature images

-b, --min-breathing-frequency=-1; float

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Registration

-L, --linear-optimizer=gsl:opt=simplex,step=1.0; factory: Optimizer used for minimization of the linear registration The string value will be used to construct a plug-in.. For supported plug-ins see Plugin type: minimizer/singlecost
--linear-transform=affine; factory: linear transform to be used The string value will be used to construct a plug-in.. For supported plug-ins see Plugin type: 2dimage/transform
-O, --non-linear-optimizer=gsl:opt=gd,step=0.1; factory: Optimizer used for minimization in the non-linear registration. The string value will be used to construct a plug-in.. For supported plug-ins see Plugin type: minimizer/singlecost
-a, --start-c-rate=16; double: start coefficinet rate in spines, gets divided by --c-rate-divider with every pass.
--c-rate-divider=2; double: Cofficient rate divider for each pass.
-d, --start-divcurl=10000; double: Start divcurl weight, gets divided by --divcurl-divider with every pass.
--divcurl-divider=2; double: Divcurl weight scaling with each new pass.
-R, --reference=-1; int: Global reference all image should be aligned to. If set to a non-negative value, the images will be aligned to this references, and the cropped output image date will be injected into the original images. Leave at -1 if you don't care. In this case all images with be registered to a mean position of the movement
-w, --imagecost=image:weight=1,cost=ssd; factory: image cost, do not specify the src and ref parameters, these will be set by the program. The string value will be used to construct a plug-in.. For supported plug-ins see Plugin type: 2dimage/fullcost
-l, --mg-levels=3; ulong: multi-resolution levels
-p, --linear-passes=3; ulong: linear registration passes (0 to disable)
-P, --nonlinear-passes=3; ulong: non-linear registration passes (0 to disable)

Example:

mia-2dmyoicapgt   -i segment.set -o registered.set -k 2

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dmyoica-nonrigid2	Home	mia-2dmyomilles

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dmyomilles.html │ │ │ @@ -1,5 +1,5 @@ │ │ │ mia-2dmyomilles

mia-2dmyomilles
Prev	Registration of series of 2D images	Next

mia-2dmyomilles

Sysnopis:

mia-2dmyomilles {-i string} {-o string} [ │ │ │ options │ │ │ ...]

Description:

This program is use to run a modified version of the ICA based registration approach described in

Milles et al. 'Fully Automated Motion Correction in First-Pass Myocardial Perfusion MR Image Sequences', Trans. Med. Imaging., 27(11), 1611-1621, 2008.

Changes include the extraction of the quasi-periodic movement in free breathingly acquired data sets and the option to run affine or rigid registration instead of the optimization of translations only. │ │ │ -

Options:

File-IO

-i, --in-file=(required, input); string: input perfusion data set
-o, --out-file=(required, output); string: output perfusion data set
-r, --registered=STRING: file name base for registered files
--save-references=STRING: save synthetic reference images to this file base
--save-cropped=STRING: save cropped image set to this file
--save-feature=STRING: save the features images resulting from the ICA and some intermediate images used for the RV-LV segmentation with the given file name base to PNG files. Also save the coefficients of the initial best and the final IC mixing matrix.

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

ICA

--fastica=internal; factory

FastICA implementationto be used. For supported plug-ins see Plugin type: fastica/implementation

-C, --components=0; ulong

ICA components 0 = automatic estimation

--normalize

normalized ICs

--no-meanstrip

don't strip the mean from the mixing curves

-g, --guess

use initial guess for myocardial perfusion

-s, --segscale=1.4; float

segment and scale the crop box around the LV (0=no segmentation)

-k, --skip=0; ulong

skip images at the beginning of the series as they are of other modalities

-m, --max-ica-iter=400; ulong

maximum number of iterations in ICA

-E, --segmethod=features; dict

Segmentation method

delta-feature:	difference of the feature images
delta-peak:	difference of the peak enhancement images
features:	feature images

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Registration

-c, --cost=ssd; stringSTRING: registration criterion
-O, --optimizer=gsl:opt=simplex,step=1.0; factory: Optimizer used for minimization. For supported plug-ins see Plugin type: minimizer/singlecost
-f, --transForm=rigid; factory: transformation type. For supported plug-ins see Plugin type: 2dimage/transform
-l, --mg-levels=3; ulong: multi-resolution levels
-R, --reference=-1; int: Global reference all image should be aligned to. If set to a non-negative value, the images will be aligned to this references, and the cropped output image date will be injected into the original images. Leave at -1 if you don't care. In this case all images with be registered to a mean position of the movement
-P, --passes=2; ulong: registration passes

Example:

Options:

File-IO

-i, --in-file=(input, required); string: input perfusion data set
-o, --out-file=(output, required); string: output perfusion data set
-r, --registered=STRING: file name base for registered files
--save-references=STRING: save synthetic reference images to this file base
--save-cropped=STRING: save cropped image set to this file
--save-feature=STRING: save the features images resulting from the ICA and some intermediate images used for the RV-LV segmentation with the given file name base to PNG files. Also save the coefficients of the initial best and the final IC mixing matrix.

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

ICA

--fastica=internal; factory

FastICA implementationto be used. For supported plug-ins see Plugin type: fastica/implementation

-C, --components=0; ulong

ICA components 0 = automatic estimation

--normalize

normalized ICs

--no-meanstrip

don't strip the mean from the mixing curves

-g, --guess

use initial guess for myocardial perfusion

-s, --segscale=1.4; float

segment and scale the crop box around the LV (0=no segmentation)

-k, --skip=0; ulong

skip images at the beginning of the series as they are of other modalities

-m, --max-ica-iter=400; ulong

maximum number of iterations in ICA

-E, --segmethod=features; dict

Segmentation method

delta-feature:	difference of the feature images
delta-peak:	difference of the peak enhancement images
features:	feature images

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Registration

-c, --cost=ssd; stringSTRING: registration criterion
-O, --optimizer=gsl:opt=simplex,step=1.0; factory: Optimizer used for minimization. For supported plug-ins see Plugin type: minimizer/singlecost
-f, --transForm=rigid; factory: transformation type. For supported plug-ins see Plugin type: 2dimage/transform
-l, --mg-levels=3; ulong: multi-resolution levels
-R, --reference=-1; int: Global reference all image should be aligned to. If set to a non-negative value, the images will be aligned to this references, and the cropped output image date will be injected into the original images. Leave at -1 if you don't care. In this case all images with be registered to a mean position of the movement
-P, --passes=2; ulong: registration passes

Example:

mia-2dmyomilles   -i segment.set -o registered.set -k 2

Author(s):

Gert Wollny

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mia-2dmyoicapgt	Home	mia-2dmyoperiodic-nonrigid

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dmyoperiodicnonrigid.html │ │ │ @@ -1,7 +1,7 @@ │ │ │ mia-2dmyoperiodic-nonrigid

mia-2dmyoperiodic-nonrigid
Prev	Registration of series of 2D images	Next

mia-2dmyoperiodic-nonrigid

Sysnopis:

mia-2dmyoperiodic-nonrigid {-i string} {-o string} [ │ │ │ options │ │ │ ...]

Description:

This program runs the non-rigid registration of an perfusion image series preferable acquired letting the patient breath freely. The registration algorithm implementes

G. Wollny, M-J Ledesma-Cabryo, P.Kellman, and A.Santos, "Exploiting Quasiperiodicity in Motion Correction of Free-Breathing," IEEE Transactions on Medical Imaging, 29(8), 2010.

Options:

│ │ │ -File-IO

-i, --in-file=(required, input); string: input perfusion data set
-o, --out-file=(required, output); string: output perfusion data set
-r, --registered=reg; stringSTRING: file name base for registered fiels
--save-references: Save synthetic references to files refXXXX.v

│ │ │ +File-IO

-i, --in-file=(input, required); string: input perfusion data set
-o, --out-file=(output, required); string: output perfusion data set
-r, --registered=reg; stringSTRING: file name base for registered fiels
--save-references: Save synthetic references to files refXXXX.v

│ │ │ Preconditions

-k, --skip=0; ulong: Skip images at the begin of the series
--max-candidates=20; ulong: maximum number of candidates for global reference image
-S, --cost-series=image:cost=[ngf:eval=ds]; factory: Const function to use for the analysis of the series. For supported plug-ins see Plugin type: 2dimage/fullcost
--ref-idx=STRING: save reference index number to this file
-R, --global-reference=-1; int: save reference index number to this file
-D, --max-subset-delta=0; ulong: Maximum delta between two elements of the prealigned subset

│ │ │ Registration

-O, --optimizer=gsl:opt=gd,step=0.01; factory: Optimizer used for minimization. For supported plug-ins see Plugin type: minimizer/singlecost
--refiner=: optimizer used for additional minimization. For supported plug-ins see Plugin type: minimizer/singlecost
-l, --mr-levels=3; ulong: multi-resolution levels
-f, --transForm=spline:rate=16,penalty=[divcurl:weight=0.01]; factory: transformation type. For supported plug-ins see Plugin type: 2dimage/transform
-1, --cost-subset=image:cost=[ngf:eval=ds]; factory: Cost function for registration during the subset registration. For supported plug-ins see Plugin type: 2dimage/fullcost
-2, --cost-final=image:cost=ssd; factory: Cost function for registration during the final registration. For supported plug-ins see Plugin type: 2dimage/fullcost

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Register the perfusion series given in 'segment.set'. Skip two images at the beginning, usa spline transformation of a knot rate 16 pixels, and penalize the transformation by divcurl with weight 5. Store the result in 'registered.set'. │ │ │

mia-2dmyoperiodic-nonrigid   -i segment.set -o registered.set -k 2 -d 5 -f spline:rate=16,penalty=[divcurl:weight=5]

Author(s):

Gert Wollny

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mia-2dmyomilles	Home	mia-2dmyopgt-nonrigid

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dmyopgtnonrigid.html │ │ │ @@ -1,6 +1,6 @@ │ │ │ mia-2dmyopgt-nonrigid

mia-2dmyopgt-nonrigid
Prev	Registration of series of 2D images	Next

mia-2dmyopgt-nonrigid

Sysnopis:

mia-2dmyopgt-nonrigid {-i string} {-o string} [ │ │ │ options │ │ │ ...]

Description:

This program implements the non-linear registration based on Pseudo Ground Thruth for motion compensation of series of myocardial perfusion images given as a data set as described in

Chao Li and Ying Sun, 'Nonrigid Registration of Myocardial Perfusion MRI Using Pseudo Ground Truth' , In Proc. Medical Image Computing and Computer-Assisted Intervention MICCAI 2009, 165-172, 2009

. Note that for this nonlinear motion correction a preceding linear registration step is usually required.

Options:

│ │ │ -File-IO

-i, --in-file=(required, input); string: input perfusion data set
-o, --out-file=(required, output); string: output perfusion data set
-r, --registered=reg; stringSTRING: file name base for registered files, the image file type is the same as given in the input data set

│ │ │ +File-IO

-i, --in-file=(input, required); string: input perfusion data set
-o, --out-file=(output, required); string: output perfusion data set
-r, --registered=reg; stringSTRING: file name base for registered files, the image file type is the same as given in the input data set

│ │ │ Pseudo Ground Thruth estimation

-A, --alpha=1; double: spacial neighborhood penalty weight
-B, --beta=1; double: temporal second derivative penalty weight
-R, --rho-thresh=0.85; double: correlation threshold for neighborhood analysis
-k, --skip=0; ulong: skip images at the beginning of the series e.g. because as they are of other modalities

│ │ │ Registration

-O, --optimizer=gsl:opt=gd,step=0.1; factory: Optimizer used for minimization. For supported plug-ins see Plugin type: minimizer/singlecost
-a, --start-c-rate=32; double: start coefficinet rate in spines, gets divided by --c-rate-divider with every pass
--c-rate-divider=4; double: cofficient rate divider for each pass
-d, --start-divcurl=20; double: start divcurl weight, gets divided by --divcurl-divider with every pass
--divcurl-divider=4; double: divcurl weight scaling with each new pass
-w, --imageweight=1; double: image cost weight
-l, --mg-levels=3; ulong: multi-resolution levels
-P, --passes=4; ulong: registration passes

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Register the perfusion series given in 'segment.set' by using Pseudo Ground Truth estimation. Skip two images at the beginning and otherwiese use the default parameters. Store the result in 'registered.set'.

mia-2dmyopgt-nonrigid -i segment.set -o registered.set -k 2

Author(s):

Gert Wollny

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│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dmyoserialnonrigid.html │ │ │ @@ -1,10 +1,10 @@ │ │ │ mia-2dmyoserial-nonrigid

mia-2dmyoserial-nonrigid
Prev	Registration of series of 2D images	Next

mia-2dmyoserial-nonrigid

Sysnopis:

mia-2dmyoserial-nonrigid {-i string} {-o string} [ │ │ │ options │ │ │ ...] [ │ │ │ │ │ │ Plugin type: 2dimage/fullcost │ │ │ │ │ │ ...]

Description:

This program runs the non-rigid motion compensation registration of an perfusion image series. The registration is run in a serial manner, this is, only images in temporal succession are registered, and the obtained transformations are applied accumulated to reach full registration. See:

Wollny, G., Ledesma-Carbayo, M.J., Kellman, P., Santos, A. "A New Similarity Measure for Non-Rigid Breathing Motion Compensation of Myocardial Perfusion MRI ". Proc 30th Annual International IEEE EMBS Conference, pp. 3389-3392. Vancouver, Aug. 2008.

Options:

│ │ │ -File-IO

-i, --in-file=(required, input); string: input perfusion data set
-o, --out-file=(required, output); string: output perfusion data set
-R, --registered=reg; stringSTRING: file name base for registered fiels

│ │ │ +File-IO

-i, --in-file=(input, required); string: input perfusion data set
-o, --out-file=(output, required); string: output perfusion data set
-R, --registered=reg; stringSTRING: file name base for registered fiels

│ │ │ Registration

-O, --optimizer=gsl:opt=gd,step=0.1; factory: Optimizer used for minimization. For supported plug-ins see Plugin type: minimizer/singlecost
-l, --mg-levels=3; ulong: multi-resolution levels
-f, --transForm=spline:rate=16,penalty=[divcurl:weight=0.01]; factory: transformation type. For supported plug-ins see Plugin type: 2dimage/transform
-r, --ref=-1; int: reference frame (-1 == use image in the middle)
-k, --skip=0; int: skip registration of these images at the beginning of the series

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Register the perfusion series given in 'segment.set' to reference image 30. Skip two images at the beginning and using mutual information as cost function, and penalize the transformation by divcurl with weight 5. Store the result in 'registered.set'. │ │ │

mia-2dmyoserial-nonrigid   -i segment.set -o registered.set -k 2  -r 30 image:cost=mi -f spline:rate=5,penalty=[divcurl:weight=5]

Author(s):

Gert Wollny

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mia-2dmyopgt-nonrigid	Home	mia-2dmyoset-all2one-nonrigid

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dmyoseriescompdice.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-2dmyoseries-compdice

mia-2dmyoseries-compdice
Prev	Tools for Myocardial Perfusion Analysis	Next

mia-2dmyoseries-compdice

Sysnopis:

mia-2dmyoseries-compdice {-1 string} {-2 string} [ │ │ │ options │ │ │ - ...]

Description:

This program is used to evaluate the per-frame dice index of segmented regions of two image series

Options:

-1, --first=(required, input); string: first segmentation set
-2, --second=(required, input); string: second segmentation set
-k, --skip=2; ulong: images to skip atthe begin of the series

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the per-frame dice index of the segmentations of set segment.set with respect to the segmentation set reference.set skipping two images at the beginning.

mia-2dmyoseries-compdice -i segment.set -r reference.set -k 2

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dmyocard-icaseries	Home	mia-2dmyoseries-dice

│ │ │ + ...]

Description:

This program is used to evaluate the per-frame dice index of segmented regions of two image series

Options:

-1, --first=(input, required); string: first segmentation set
-2, --second=(input, required); string: second segmentation set
-k, --skip=2; ulong: images to skip atthe begin of the series

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the per-frame dice index of the segmentations of set segment.set with respect to the segmentation set reference.set skipping two images at the beginning.

mia-2dmyoseries-compdice -i segment.set -r reference.set -k 2

Author(s):

Gert Wollny

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mia-2dmyocard-icaseries	Home	mia-2dmyoseries-dice

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dmyoseriesdice.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-2dmyoseries-dice

mia-2dmyoseries-dice
Prev	Tools for Myocardial Perfusion Analysis	Next

mia-2dmyoseries-dice

Sysnopis:

mia-2dmyoseries-dice {-i string} [ │ │ │ options │ │ │ - ...]

Description:

This program is used to evaluate the per-frame dice index of segmented regions of an image with respect to the segmentation of a reference frame from the same series.

Options:

-i, --input=(required, input); string: original segmentation set
-k, --skip=2; int: images to skip atthe bgin of the series
-r, --reference=20; ulong: reference image

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the dice index of segmentation set segment.set with reference 30 and skipping the first two frames.

mia-2dmyoseries-dice -i segment.set -r 30 -k 2

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dmyoseries-compdice	Home	mia-2dsegcompare

│ │ │ + ...]

Description:

This program is used to evaluate the per-frame dice index of segmented regions of an image with respect to the segmentation of a reference frame from the same series.

Options:

-i, --input=(input, required); string: original segmentation set
-k, --skip=2; int: images to skip atthe bgin of the series
-r, --reference=20; ulong: reference image

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the dice index of segmentation set segment.set with reference 30 and skipping the first two frames.

mia-2dmyoseries-dice -i segment.set -r 30 -k 2

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dmyoseries-compdice	Home	mia-2dsegcompare

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dmyosetall2onenonrigid.html │ │ │ @@ -1,10 +1,10 @@ │ │ │ mia-2dmyoset-all2one-nonrigid

mia-2dmyoset-all2one-nonrigid
Prev	Registration of series of 2D images	Next

mia-2dmyoset-all2one-nonrigid

Sysnopis:

mia-2dmyoset-all2one-nonrigid {-i string} {-o string} [ │ │ │ options │ │ │ ...] [ │ │ │ │ │ │ Plugin type: 2dimage/fullcost │ │ │ │ │ │ ...]

Description:

This program runs non-rigid registration of a series of images given in an image set. All images are registered to one user defined reference image.

Options:

│ │ │ -File-IO

-i, --in-file=(required, input); string: input perfusion data set
-o, --out-file=(required, output); string: output perfusion data set
--out-filebase=reg; stringSTRING: file name basae for registered files, file type is deducted from the image file type in the input data set.

│ │ │ +File-IO

-i, --in-file=(input, required); string: input perfusion data set
-o, --out-file=(output, required); string: output perfusion data set
--out-filebase=reg; stringSTRING: file name basae for registered files, file type is deducted from the image file type in the input data set.

│ │ │ Registration

-k, --skip=0; int: Skip images at the beginning of the series
-O, --optimizer=gsl:opt=gd,step=0.1; stringSTRING: Optimizer used for minimization
-l, --mg-levels=3; ulong: multi-resolution levels
-f, --transForm=spline; factory: transformation type. For supported plug-ins see Plugin type: 2dimage/transform
-r, --ref=-1; int: reference frame (-1 == use image in the middle)

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Register the perfusion series given in segment.set by optimizing a spline based transformation with a coefficient rate of 16 pixel using Mutual Information and penalize the transformation by using divcurl with aweight of 2.0.

mia-2dmyoset-all2one-nonrigid -i segment.set -o registered.set 
│ │ │      -f spline:rate=16,penalty=[divcurl:weight=2.0] image:cost=mi,weight=2.0

Author(s):

Gert Wollny

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mia-2dmyoserial-nonrigid	Home	Tools for the Analysis of 2D image series

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dsegcompare.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-2dsegcompare

mia-2dsegcompare
Prev	Tools for Myocardial Perfusion Analysis	Next

mia-2dsegcompare

Sysnopis:

mia-2dsegcompare {-i string} {-r string} [ │ │ │ options │ │ │ - ...]

Description:

This program is used to evaluate the Hausdorff distance between each frame of a perfusion time series of the input set to the corresponding frame of the reference set and prints the result to stdout.

Options:

-i, --in-file=(required, input); string: input segmentation set
-r, --ref-file=(required, input); string: reference segmentation set

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the per-slice Hausdorff distance of input.set and reference.set.

mia-2dsegcompare -i input.set -r reference.set

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dmyoseries-dice	Home	mia-2dseghausdorff

│ │ │ + ...]

Description:

This program is used to evaluate the Hausdorff distance between each frame of a perfusion time series of the input set to the corresponding frame of the reference set and prints the result to stdout.

Options:

-i, --in-file=(input, required); string: input segmentation set
-r, --ref-file=(input, required); string: reference segmentation set

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the per-slice Hausdorff distance of input.set and reference.set.

mia-2dsegcompare -i input.set -r reference.set

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dmyoseries-dice	Home	mia-2dseghausdorff

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dseghausdorff.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-2dseghausdorff

mia-2dseghausdorff
Prev	Tools for Myocardial Perfusion Analysis	Next

mia-2dseghausdorff

Sysnopis:

mia-2dseghausdorff {-i string} {-r ulong} [ │ │ │ options │ │ │ - ...]

Description:

Get the per-slice Hausdorff distance of a segmentation with respect to a given reference frame and print it to stdout.

Options:

-i, --in-file=(required, input); string: input segmentation set
-r, --ref-frame=(required); ulong: reference frame
-k, --skip=0; int: skip frames at the beginning

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the Hausdorff distance of the segmentations of set segment.set with respect to the segmentation given in frame 20.

mia-2dseghausdorff  -i segment.set -r 20

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dsegcompare	Home	mia-2dsegmentcropbox

│ │ │ + ...]

Description:

Get the per-slice Hausdorff distance of a segmentation with respect to a given reference frame and print it to stdout.

Options:

-i, --in-file=(input, required); string: input segmentation set
-r, --ref-frame=(required); ulong: reference frame
-k, --skip=0; int: skip frames at the beginning

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the Hausdorff distance of the segmentations of set segment.set with respect to the segmentation given in frame 20.

mia-2dseghausdorff  -i segment.set -r 20

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dsegcompare	Home	mia-2dsegmentcropbox

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dsegmentahmed.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-2dsegment-ahmed

mia-2dsegment-ahmed
Prev	Analysis, filtering, combining, and segmentation of 2D images	Next

mia-2dsegment-ahmed

Sysnopis:

mia-2dsegment-ahmed {-i io} {-o io} [ │ │ │ options │ │ │ - ...]

Description:

This program implements a variation of the paper:

Mohamed N. Ahmed et. al, "A Modified Fuzzy C-Means Algorithm for Bias Field estimation and Segmentation of MRI Data", IEEE Trans. on Medical Imaging, Vol. 21, No. 3, March 2002,

changes are: p=2, and exp

Options:

-i, --in-file=(required, input); io: image to be segmented. For supported file types see Plugin type: 2dimage/io
-o, --out-file=(required, output); io: class probability images, the image type must support multiple images and floating point values. For supported file types see Plugin type: 2dimage/io
-a, --no-of-classes=3; int: number of classes
-b, --bias-correct: apply bias field correction
-c, --class-centres=: initial class centers
-s, --spread=64; float: spread parameter describing the strength of mattar distinction

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run a 5-class segmentation over input image input.v and store the class probability images in cls.v.

mia-2dsegment-ahmed -i input.v -a 5 -o cls.v

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dmultiimagevar	Home	mia-2dsegment-fuzzyw

│ │ │ + ...]

Description:

This program implements a variation of the paper:

Mohamed N. Ahmed et. al, "A Modified Fuzzy C-Means Algorithm for Bias Field estimation and Segmentation of MRI Data", IEEE Trans. on Medical Imaging, Vol. 21, No. 3, March 2002,

changes are: p=2, and exp

Options:

-i, --in-file=(input, required); io: image to be segmented. For supported file types see Plugin type: 2dimage/io
-o, --out-file=(output, required); io: class probability images, the image type must support multiple images and floating point values. For supported file types see Plugin type: 2dimage/io
-a, --no-of-classes=3; int: number of classes
-b, --bias-correct: apply bias field correction
-c, --class-centres=: initial class centers
-s, --spread=64; float: spread parameter describing the strength of mattar distinction

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run a 5-class segmentation over input image input.v and store the class probability images in cls.v.

mia-2dsegment-ahmed -i input.v -a 5 -o cls.v

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dmultiimagevar	Home	mia-2dsegment-fuzzyw

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dsegmentcropbox.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-2dsegmentcropbox

mia-2dsegmentcropbox
Prev	Tools for Myocardial Perfusion Analysis	Next

mia-2dsegmentcropbox

Sysnopis:

mia-2dsegmentcropbox {-i string} {-o string} [ │ │ │ options │ │ │ - ...]

Description:

This program is used on a segmentation set and evaluates a bounding box that encloses the segmentation in all slices. This bounding box is then used to crop the original images, correct the segmentation and store a new segmentation set with the cropped images. The cropped images will be of the same type as the original images. If no segmentation is given in the set, the result is undefined.

Options:

-i, --in-file=(required, input); string: input segmentation set
-p, --override-imagepath: Instead of using the path of the image files as given in the segmentation set, assume the files are located in the current directory
-o, --out-file=(required, output); string: output segmentation set
-c, --cropped-base=crop; stringSTRING: Base name for the cropped image files, the file type and numbering will be based on the input image file type and numbering.
-e, --enlarge=5; float: Enlarge the area around the obtained sbounding box by this number of pixels in each direction

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the optimal cropping for a segmentation set segment.set and enlarge it by 3 pixels. Store the resulting set in the file cropped.set.

mia-2dsegmentcropbox -i segment.set -o cropped.set -e 3

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dseghausdorff	Home	mia-2dsegseriesstats

│ │ │ + ...]

Description:

Options:

-i, --in-file=(input, required); string: input segmentation set
-p, --override-imagepath: Instead of using the path of the image files as given in the segmentation set, assume the files are located in the current directory
-o, --out-file=(output, required); string: output segmentation set
-c, --cropped-base=crop; stringSTRING: Base name for the cropped image files, the file type and numbering will be based on the input image file type and numbering.
-e, --enlarge=5; float: Enlarge the area around the obtained sbounding box by this number of pixels in each direction

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the optimal cropping for a segmentation set segment.set and enlarge it by 3 pixels. Store the resulting set in the file cropped.set.

mia-2dsegmentcropbox -i segment.set -o cropped.set -e 3

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dseghausdorff	Home	mia-2dsegseriesstats

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dsegmentfuzzyw.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-2dsegment-fuzzyw

mia-2dsegment-fuzzyw
Prev	Analysis, filtering, combining, and segmentation of 2D images	Next

mia-2dsegment-fuzzyw

Sysnopis:

mia-2dsegment-fuzzyw {-i io} [ │ │ │ options │ │ │ - ...]

Description:

This program is a implementation of a fuzzy c-means segmentation algorithm

Options:

File I/O

-i, --in-file=(required, input); io: image to be segmented. For supported file types see Plugin type: 2dimage/io
-c, --cls-file=(output); io: class probability images, the image type must support multiple images and floating point values. For supported file types see Plugin type: 2dimage/io
-o, --out-file=(output); io: B-field corrected image. For supported file types see Plugin type: 2dimage/io
-g, --gain-log-file=(output); io: Logarithmic gain field, the image type must support floating point values. For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Segmentation parameters

-n, --no-of-classes=3; uint: number of classes to segment
-C, --class-centres=: initial class centers
-N, --neighborhood=shmean:shape=8n; factory: neighborhood filter for B-field correction. For supported plug-ins see Plugin type: 2dimage/filter
-a, --alpha=0.7; float: weight of neighborhood filter for B-field correction
-p, --fuzziness=2; float: parameter describing the fuzzyness of mattar distinction
-e, --epsilon=0.01; float: Stopping criterion for class center estimation.

Example:

Run a 5-class segmentation over inpt image input.v and store the class probability images in cls.v.

mia-2dsegment-fuzzyw -i input.v -a 5 -o cls.v

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dsegment-ahmed	Home	mia-2dsegment-local-cmeans

│ │ │ + ...]

Description:

This program is a implementation of a fuzzy c-means segmentation algorithm

Options:

File I/O

-i, --in-file=(input, required); io: image to be segmented. For supported file types see Plugin type: 2dimage/io
-c, --cls-file=(output); io: class probability images, the image type must support multiple images and floating point values. For supported file types see Plugin type: 2dimage/io
-o, --out-file=(output); io: B-field corrected image. For supported file types see Plugin type: 2dimage/io
-g, --gain-log-file=(output); io: Logarithmic gain field, the image type must support floating point values. For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Segmentation parameters

-n, --no-of-classes=3; uint: number of classes to segment
-C, --class-centres=: initial class centers
-N, --neighborhood=shmean:shape=8n; factory: neighborhood filter for B-field correction. For supported plug-ins see Plugin type: 2dimage/filter
-a, --alpha=0.7; float: weight of neighborhood filter for B-field correction
-p, --fuzziness=2; float: parameter describing the fuzzyness of mattar distinction
-e, --epsilon=0.01; float: Stopping criterion for class center estimation.

Example:

Run a 5-class segmentation over inpt image input.v and store the class probability images in cls.v.

mia-2dsegment-fuzzyw -i input.v -a 5 -o cls.v

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dsegment-ahmed	Home	mia-2dsegment-local-cmeans

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dsegmentlocalcmeans.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-2dsegment-local-cmeans

mia-2dsegment-local-cmeans
Prev	Analysis, filtering, combining, and segmentation of 2D images	Next

mia-2dsegment-local-cmeans

Sysnopis:

mia-2dsegment-local-cmeans {-i io} [ │ │ │ options │ │ │ - ...]

Description:

This program runs the segmentation of a 2D image by applying a localized c-means approach that helps to overcome intensity inhomogeneities in the image. The approach evaluates a global c-means clustering, and then separates the image into overlapping regions where more c-means iterations are run only including the locally present classes, i.e. the classes that relatively contain more pixels than a given threshold. This program implements a 2D prototype of the algorithm described in:

Dunmore CJ, Wollny G, Skinner MM. (2018) MIA-Clustering: a novel method for segmentation of paleontological material. PeerJ 6:e4374.

Options:

File-IO

-i, --in-file=(required, input); io: image to be segmented. For supported file types see Plugin type: 2dimage/io
-o, --out-file=(output); io: class label image based on merging local labels. For supported file types see Plugin type: 2dimage/io
-G, --out-global-crisp=(output); io: class label image based on global segmentation. For supported file types see Plugin type: 2dimage/io
-C, --class-prob=(output); io: class probability image file, filetype must support floating point multi-frame images. For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Parameters

-g, --grid-spacing=15; int in [3, inf): Spacing of the grid used to modulate the intensity inhomogeneities
-c, --cmeans=kmeans:nc=3; factory: c-means initializer. For supported plug-ins see Plugin type: 1d/cmeans
-e, --c-means-epsilon=0.0001; float in (0, inf): c-means breaking condition for update tolerance
-t, --relative-cluster-threshold=0.02; double in [0, 1): threshhold to ignore classes when initializing the local cmeans from the global one.

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run the segmentation on image test.png using three classes, local regions of 40 pixels (grid width 20 pixels), and a class ignore threshold of 0.01.

mia-2dsegment-local-cmeans -i test.png -o label.png -n 3 -g 20 -t 0.01

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dsegment-fuzzyw	Home	mia-2dsegment-local-kmeans

│ │ │ + ...]

Description:

Dunmore CJ, Wollny G, Skinner MM. (2018) MIA-Clustering: a novel method for segmentation of paleontological material. PeerJ 6:e4374.

Options:

File-IO

-i, --in-file=(input, required); io: image to be segmented. For supported file types see Plugin type: 2dimage/io
-o, --out-file=(output); io: class label image based on merging local labels. For supported file types see Plugin type: 2dimage/io
-G, --out-global-crisp=(output); io: class label image based on global segmentation. For supported file types see Plugin type: 2dimage/io
-C, --class-prob=(output); io: class probability image file, filetype must support floating point multi-frame images. For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Parameters

-g, --grid-spacing=15; int in [3, inf): Spacing of the grid used to modulate the intensity inhomogeneities
-c, --cmeans=kmeans:nc=3; factory: c-means initializer. For supported plug-ins see Plugin type: 1d/cmeans
-e, --c-means-epsilon=0.0001; float in (0, inf): c-means breaking condition for update tolerance
-t, --relative-cluster-threshold=0.02; double in [0, 1): threshhold to ignore classes when initializing the local cmeans from the global one.

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run the segmentation on image test.png using three classes, local regions of 40 pixels (grid width 20 pixels), and a class ignore threshold of 0.01.

mia-2dsegment-local-cmeans -i test.png -o label.png -n 3 -g 20 -t 0.01

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dsegment-fuzzyw	Home	mia-2dsegment-local-kmeans

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dsegmentlocalkmeans.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-2dsegment-local-kmeans

mia-2dsegment-local-kmeans
Prev	Analysis, filtering, combining, and segmentation of 2D images	Next

mia-2dsegment-local-kmeans

Sysnopis:

mia-2dsegment-local-kmeans {-i io} [ │ │ │ options │ │ │ - ...]

Description:

This program runs the segmentation of a 2D image by applying a localized k-means approach that helps to overcome intensity inhomogeneities in the image. The approach evaluates a global k-means clustering, and then separates the image into overlapping regions where more k-means iterations are run only including the locally present classes, i.e. the classes that relatively contain more pixels than a given threshold.

Options:

File-IO

-i, --in-file=(required, input); io: image to be segmented. For supported file types see Plugin type: 2dimage/io
-o, --out-file=(output); io: class label image based on merging local labels. For supported file types see Plugin type: 2dimage/io
-O, --out-file2=(output); io: class label image based on classifying by using the interpolated class centers . For supported file types see Plugin type: 2dimage/io
-D, --debug-centers=(output); io: Save the class center images to a debug file (type is double). For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Parameters

-g, --grid-spacing=20; int in [3, inf): Spacing of the grid used to modulate the intensity inhomogeneities
-n, --nclasses=3; uint in [2, 127]: Number of intensity classes to segment
-t, --relative-cluster-threshold=0.0001; double in [0, 1): Number of intensity classes to segment

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run the segmentation on image test.png using three classes, local regions of 40 pixels (grid width 20 pixels), and a class ignore threshold of 0.01.

mia-2dsegment-local-kmeans -i test.png -o label.png -n 3 -g 20 -t 0.01

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dsegment-local-cmeans	Home	mia-2dsegment-per-pixel-kmeans

│ │ │ + ...]

Description:

Options:

File-IO

-i, --in-file=(input, required); io: image to be segmented. For supported file types see Plugin type: 2dimage/io
-o, --out-file=(output); io: class label image based on merging local labels. For supported file types see Plugin type: 2dimage/io
-O, --out-file2=(output); io: class label image based on classifying by using the interpolated class centers . For supported file types see Plugin type: 2dimage/io
-D, --debug-centers=(output); io: Save the class center images to a debug file (type is double). For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Parameters

-g, --grid-spacing=20; int in [3, inf): Spacing of the grid used to modulate the intensity inhomogeneities
-n, --nclasses=3; uint in [2, 127]: Number of intensity classes to segment
-t, --relative-cluster-threshold=0.0001; double in [0, 1): Number of intensity classes to segment

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run the segmentation on image test.png using three classes, local regions of 40 pixels (grid width 20 pixels), and a class ignore threshold of 0.01.

mia-2dsegment-local-kmeans -i test.png -o label.png -n 3 -g 20 -t 0.01

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dsegment-local-cmeans	Home	mia-2dsegment-per-pixel-kmeans

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dsegmentperpixelkmeans.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-2dsegment-per-pixel-kmeans

mia-2dsegment-per-pixel-kmeans
Prev	Analysis, filtering, combining, and segmentation of 2D images	Next

mia-2dsegment-per-pixel-kmeans

Sysnopis:

mia-2dsegment-per-pixel-kmeans {-i io} {-o io} [ │ │ │ options │ │ │ - ...]

Description:

Options:

File-IO

-i, --in-file=(required, input); io: image to be segmented. For supported file types see Plugin type: 2dimage/io
-o, --out-file=(required, output); io: class label image based on merging local labels. For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Parameters

-w, --window=20; int in [3, inf): Window size around the pixel to be analyzed
-n, --nclasses=3; uint in [2, 127]: Number of intensity classes to segment
-t, --relative-cluster-threshold=0.0001; double in [0, 1): Number of intensity classes to segment

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run the segmentation on image test.png using three classes, local regions of 40 pixels (grid width 20 pixels), and a class ignore threshold of 0.01.

mia-2dsegment-per-pixel-kmeans -i test.png -o label.png -n 3 -g 20 -t 0.01

Author(s):

Gert Wollny

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mia-2dsegment-local-kmeans	Home	Registration, Comparison, and Transformation of 2D images

│ │ │ + ...]

Description:

Options:

File-IO

-i, --in-file=(input, required); io: image to be segmented. For supported file types see Plugin type: 2dimage/io
-o, --out-file=(output, required); io: class label image based on merging local labels. For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Parameters

-w, --window=20; int in [3, inf): Window size around the pixel to be analyzed
-n, --nclasses=3; uint in [2, 127]: Number of intensity classes to segment
-t, --relative-cluster-threshold=0.0001; double in [0, 1): Number of intensity classes to segment

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run the segmentation on image test.png using three classes, local regions of 40 pixels (grid width 20 pixels), and a class ignore threshold of 0.01.

mia-2dsegment-per-pixel-kmeans -i test.png -o label.png -n 3 -g 20 -t 0.01

Author(s):

Gert Wollny

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mia-2dsegment-local-kmeans	Home	Registration, Comparison, and Transformation of 2D images

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dsegseriesstats.html │ │ │ @@ -1,7 +1,7 @@ │ │ │ mia-2dsegseriesstats

mia-2dsegseriesstats
Prev	Tools for Myocardial Perfusion Analysis	Next

mia-2dsegseriesstats

Sysnopis:

mia-2dsegseriesstats {-o string} {-g string} [ │ │ │ options │ │ │ - ...]

Description:

This program is used evaluate various time-intensity curves over a series of images given by a segmentation set. Specifically, the program is taylored to evaluate average intensities and variations of sections the left ventricle myocardium. The segmentation set must contain the segmentations for all slices that will be accessed during evaluation.

Options:

-o, --original=(required, input); string: original segmentation set
-g, --registered=(required, input); string: registered segmentation set
-k, --skip=2; int: images to skip at the begin of the series, if (k < 0) use RV peak of the registered set if set
-r, --reference=-1; int: reference frame for automatic curve extraction. Negative values can be used to indicate specific values (if given in the segmentation set): │ │ │ + ...]

Description:

Options:

-o, --original=(input, required); string: original segmentation set
-g, --registered=(input, required); string: registered segmentation set
-k, --skip=2; int: images to skip at the begin of the series, if (k < 0) use RV peak of the registered set if set
-r, --reference=-1; int: reference frame for automatic curve extraction. Negative values can be used to indicate specific values (if given in the segmentation set): │ │ │ -3: Middle of the series │ │ │ -2: prefererred reference │ │ │ -1: LV peak │ │ │ if any of the above is not available or the value is < -3, use the last frame of the series.
-c, --curves=(output); string: region average value curves, The output files each comprises a table in plain-text format that contains three columns for each section of the LV myocardium: The first column contains the values obtained by using the original segmentation of the reference on all images of the original series, the second column contains the values obtained by the registered segmentation of the reference on all images of the registered series, and the third column contains the values obtained by using the segmentations of each slice on the original images.
-v, --varcurves=(output); string: region variation values, same formt as described above.
-n, --nsections=0; ulong: number of sections to use, 0=use as segmented, otherwise Otherwise, the LV myocardium is divided into n sections that enclose equal angles starting at the right ventricle insertion point moving clock-wise using the LV center as angular point.

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the two curve typed for 12 sections from segemntation sets orig.set and reg.set skipping the first 2 frames. The output will be written to curves.txt and varcurves.txt respectively.

mia-2dsegseriesstats -i org.set -g reg.set -c curves.txt -v varcurves.txt -n 12 -k 2

Author(s):

Gert Wollny

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mia-2dsegmentcropbox	Home	mia-2dsegshift

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dsegshift.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-2dsegshift

mia-2dsegshift
Prev	Tools for Myocardial Perfusion Analysis	Next

mia-2dsegshift

Sysnopis:

mia-2dsegshift {-i io} {-o io} [ │ │ │ options │ │ │ - ...]

Description:

This program move the segmentation(s) of an image series by using a shift that is equal for all slices. The program also may remove images from the begin of the series. The program can be used to correct the segmentation of the images if the images where cropped.

Options:

-i, --in-file=(required, input); io: input segmentation set. For supported file types see Plugin type: 2dimage/io
-o, --out-file=(required, output); io: input segmentation set. For supported file types see Plugin type: 2dimage/io
-g, --image-file=crop; stringSTRING: output image filename base
-S, --shift=[0,0]; 2dfvector: shift of segmentation
-k, --skip=2; ulong: skip frames at the beginning

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Shift the segmentations of a set segement.set by -20 pixels in horizontal direction and -30 pixels in vertical direction (as if the images where cropped starting at (20,30) and store it in translate.set. The shiftes files are named translatedXXXX.png

mia-2dsegshift -i segment.set -o translate.set -g translated -S "<20,30>"

Author(s):

Gert Wollny

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mia-2dsegseriesstats	Home	mia-2dsegshiftperslice

│ │ │ + ...]

Description:

Options:

-i, --in-file=(input, required); io: input segmentation set. For supported file types see Plugin type: 2dimage/io
-o, --out-file=(output, required); io: input segmentation set. For supported file types see Plugin type: 2dimage/io
-g, --image-file=crop; stringSTRING: output image filename base
-S, --shift=[0,0]; 2dfvector: shift of segmentation
-k, --skip=2; ulong: skip frames at the beginning

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

mia-2dsegshift -i segment.set -o translate.set -g translated -S "<20,30>"

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dsegseriesstats	Home	mia-2dsegshiftperslice

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dsegshiftperslice.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-2dsegshiftperslice

mia-2dsegshiftperslice
Prev	Tools for Myocardial Perfusion Analysis	Next

mia-2dsegshiftperslice

Sysnopis:

mia-2dsegshiftperslice {-i string} {-o string} {-S string} [ │ │ │ options │ │ │ - ...]

Description:

This program move the segmentation(s) of an image series by using a shift that is given on a per-slice base. The program can be used to correct the segmentation of the images if a linear registration was executed that only applies a translation and does not correct the segmentation automatically.

Options:

-i, --in-file=(required, input); string: input segmentation set
-o, --out-file=(required, output); string: output segmentation set
-g, --image-file=crop; stringSTRING: output image filename base
-S, --shift=(required); string: shift of segmentation - base name

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Shirt the segmentation given in set segment.set by files shiftXXXX.txt and store the result in shifted.set. Note, the numbering of the shiftXXXX.txx files must coincide.

mia-2dsegshiftperslice -i segment.set -o shifted.set -g shifted -S shift

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dsegshift	Home	mia-2dseries-mincorr

│ │ │ + ...]

Description:

Options:

-i, --in-file=(input, required); string: input segmentation set
-o, --out-file=(output, required); string: output segmentation set
-g, --image-file=crop; stringSTRING: output image filename base
-S, --shift=(required); string: shift of segmentation - base name

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Shirt the segmentation given in set segment.set by files shiftXXXX.txt and store the result in shifted.set. Note, the numbering of the shiftXXXX.txx files must coincide.

mia-2dsegshiftperslice -i segment.set -o shifted.set -g shifted -S shift

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dsegshift	Home	mia-2dseries-mincorr

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dseries2dordermedian.html │ │ │ @@ -1,7 +1,7 @@ │ │ │ mia-2dseries2dordermedian

mia-2dseries2dordermedian
Prev	Tools for Myocardial Perfusion Analysis	Next

mia-2dseries2dordermedian

Sysnopis:

mia-2dseries2dordermedian {-i string} {-o io} [ │ │ │ options │ │ │ ...] [ │ │ │ │ │ │ Plugin type: 2dimage/filter │ │ │ │ │ │ - ...]

Description:

This program evaluates the pixel-wise median of the absolute values of the gauss filtered 2nd order temporal derivative of a series of images. In addition, it can be used to output the time-intensity curve of a given pixel.The program supports slice-wise spacial pre-filtering by giving additional filters as free parameters (filter/2dimage).

Options:

-i, --in-file=(required, input); string: input segmentation set
-o, --out-file=(required, output); io: output image name. For supported file types see Plugin type: 2dimage/io
-k, --skip=0; ulong: Skip files at the beginning
-e, --enlarge-boundary=5; ulong: Enlarge cropbox by number of pixels
-c, --crop: crop image before running statistics
-g, --gauss=1; ulong: gauss filter width for moothing the gradient
--itc-file=STRING: intensity time curve output file
--itc-loc=[0,0]; 2dbounds: intensity time curve output pixel coordinates

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the median of the 2nd order derivative of the series given in segmentation set segment.set after filtering with a Gaussian of width 3. In addition write the time intensity curve of pixel <128,64> to curve.txt.

mia-2dseries2dordermedian -i segment.set -o gradmedian.exr -g 1 --itc-file curve.txt --itc-loc "<128,64>"

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dseries-segdistance	Home	mia-2dseries2sets

│ │ │ + ...]

Description:

Options:

-i, --in-file=(input, required); string: input segmentation set
-o, --out-file=(output, required); io: output image name. For supported file types see Plugin type: 2dimage/io
-k, --skip=0; ulong: Skip files at the beginning
-e, --enlarge-boundary=5; ulong: Enlarge cropbox by number of pixels
-c, --crop: crop image before running statistics
-g, --gauss=1; ulong: gauss filter width for moothing the gradient
--itc-file=STRING: intensity time curve output file
--itc-loc=[0,0]; 2dbounds: intensity time curve output pixel coordinates

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

mia-2dseries2dordermedian -i segment.set -o gradmedian.exr -g 1 --itc-file curve.txt --itc-loc "<128,64>"

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dseries-segdistance	Home	mia-2dseries2sets

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dseries2sets.html │ │ │ @@ -1,7 +1,7 @@ │ │ │ mia-2dseries2sets

mia-2dseries2sets
Prev	Tools for Myocardial Perfusion Analysis	Next

mia-2dseries2sets

Sysnopis:

mia-2dseries2sets {-o string} [ │ │ │ options │ │ │ ...] [ │ │ │ │ │ │ Plugin type: 2dimage/io │ │ │ │ │ │ - ...]

Description:

This program takes all image files that are given as free parameters on the command line and creates segmentation sets based on information found in the images. Used information is the z-location of the slice and the acquisition number. The code is taylored to used the according descriptors defined in the DICOM standard. All images with the same slice location will be grouped together in one segmentation set and ordered according to their acquisition number. Slice locations are rounded to three digits accuracy to make proper comparison of floating point values feasible.

Options:

-o, --out-directory=(required, output); string: output directory (needs to exist and be writable)
--no-copy: don't copy image files to output directory

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Create the segmentation sets from a series of DICOM images and copy the files to the output directory (copying is the default).

mia-2dseries2sets -o /home/user/series /net/dicoms/patient1/series1/*.dcm

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dseries2dordermedian	Home	mia-2dseriescorr

│ │ │ + ...]

Description:

Options:

-o, --out-directory=(output, required); string: output directory (needs to exist and be writable)
--no-copy: don't copy image files to output directory

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Create the segmentation sets from a series of DICOM images and copy the files to the output directory (copying is the default).

mia-2dseries2sets -o /home/user/series /net/dicoms/patient1/series1/*.dcm

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dseries2dordermedian	Home	mia-2dseriescorr

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dseriescorr.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-2dseriescorr

mia-2dseriescorr
Prev	Tools for Myocardial Perfusion Analysis	Next

mia-2dseriescorr

Sysnopis:

mia-2dseriescorr {-i io} {-o io} [ │ │ │ options │ │ │ - ...]

Description:

Given a set of images of temporal sucession, evaluates images that represent the time-intensity correlation in horizontal and vertical direction as well as average correlation of each pixel with its neighbors. All input images must be of the same pixel type and size.

Options:

-i, --in-base=(required, input); io: input file name base. For supported file types see Plugin type: 2dimage/io
-o, --outname=(required, output); io: output file name to save the avarage per-pixel correlation. For supported file types see Plugin type: 2dimage/io
-z, --horizontal=(output); io: horiZontal correlation output file name. For supported file types see Plugin type: 2dimage/io
-t, --vertical=(output); io: verTical correlation output file name. For supported file types see Plugin type: 2dimage/io
-k, --skip=2; ulong: skip images at beginning of series
-e, --end=60; ulong: last image in series

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the time-intensity correaltions for an image series imageXXXX.png starting at image 2 and stop at image 30. Store the results in horizontal.exr, and vertical.exr.

mia-2dseriescorr -i image0000.png -k 2 -e 30 -z horizontal.exr -t vertical.exr

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dseries2sets	Home	mia-2dseriesgradMAD

│ │ │ + ...]

Description:

Options:

-i, --in-base=(input, required); io: input file name base. For supported file types see Plugin type: 2dimage/io
-o, --outname=(output, required); io: output file name to save the avarage per-pixel correlation. For supported file types see Plugin type: 2dimage/io
-z, --horizontal=(output); io: horiZontal correlation output file name. For supported file types see Plugin type: 2dimage/io
-t, --vertical=(output); io: verTical correlation output file name. For supported file types see Plugin type: 2dimage/io
-k, --skip=2; ulong: skip images at beginning of series
-e, --end=60; ulong: last image in series

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the time-intensity correaltions for an image series imageXXXX.png starting at image 2 and stop at image 30. Store the results in horizontal.exr, and vertical.exr.

mia-2dseriescorr -i image0000.png -k 2 -e 30 -z horizontal.exr -t vertical.exr

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dseries2sets	Home	mia-2dseriesgradMAD

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dseriesgradMAD.html │ │ │ @@ -1,7 +1,7 @@ │ │ │ mia-2dseriesgradMAD

mia-2dseriesgradMAD
Prev	Tools for Myocardial Perfusion Analysis	Next

mia-2dseriesgradMAD

Sysnopis:

mia-2dseriesgradMAD {-i string} {-o io} [ │ │ │ options │ │ │ ...] [ │ │ │ │ │ │ Plugin type: 2dimage/filter │ │ │ │ │ │ - ...]

Description:

Given a set of images of temporal sucession, evaluates the pixel-wise temporal gradient and then its median average distance (MAD) and stores the result in an image. Spacial pre-filtering may be applied as given additional plugin(s) (filter/2dimage).

Options:

-i, --in-file=(required, input); string: input segmentation set
-o, --out-file=(required, output); io: output file name. For supported file types see Plugin type: 2dimage/io
-k, --skip=0; ulong: Skip files at the beginning
-e, --enlarge-boundary=5; ulong: Enlarge cropbox by number of pixels
-c, --crop: crop image before running statistics

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the MAD-image of the bounding box surrounding the segmentation from a series segment.set. No spacial filtering will be applied. The bounding box will be enlarged by 3 pixels in all directions. Store the image in OpenEXR format.

mia-2dseriesgradMAD  -i segment.set -o mad.exr -c -e 3

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dseriescorr	Home	mia-2dseriesgradvariation

│ │ │ + ...]

Description:

Options:

-i, --in-file=(input, required); string: input segmentation set
-o, --out-file=(output, required); io: output file name. For supported file types see Plugin type: 2dimage/io
-k, --skip=0; ulong: Skip files at the beginning
-e, --enlarge-boundary=5; ulong: Enlarge cropbox by number of pixels
-c, --crop: crop image before running statistics

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

mia-2dseriesgradMAD  -i segment.set -o mad.exr -c -e 3

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dseriescorr	Home	mia-2dseriesgradvariation

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dseriesgradvariation.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-2dseriesgradvariation

mia-2dseriesgradvariation
Prev	Tools for Myocardial Perfusion Analysis	Next

mia-2dseriesgradvariation

Sysnopis:

mia-2dseriesgradvariation {-i string} {-o io} [ │ │ │ options │ │ │ - ...]

Description:

Given a set of images of temporal sucession, this program evaluates the gradient variation of the pixel-wise time-intensity curves of this series. If the input image set provides a segmentation, then this segmentation can be used to create a bounding box and restrict evaluation to this box.

Options:

-i, --in-file=(required, input); string: input segmentation set
-o, --out-file=(required, output); io: output file name. For supported file types see Plugin type: 2dimage/io
-k, --skip=0; ulong: Skip files at the beginning
-e, --enlarge-boundary=5; ulong: Enlarge cropbox by number of pixels
-c, --crop: crop image before running statistics

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the gradient-variation image of the bounding box surrounding the segmentation from a series 'segment.set'. The bounding box will be enlarged by 3 pixels in all directions. Store the image in OpenEXR format.

mia-2dseriesgradvariation  -i segment.set -o gradvar.exr -c -e 3

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dseriesgradMAD	Home	mia-2dserieshausdorff

│ │ │ + ...]

Description:

Options:

-i, --in-file=(input, required); string: input segmentation set
-o, --out-file=(output, required); io: output file name. For supported file types see Plugin type: 2dimage/io
-k, --skip=0; ulong: Skip files at the beginning
-e, --enlarge-boundary=5; ulong: Enlarge cropbox by number of pixels
-c, --crop: crop image before running statistics

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

mia-2dseriesgradvariation  -i segment.set -o gradvar.exr -c -e 3

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dseriesgradMAD	Home	mia-2dserieshausdorff

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dserieshausdorff.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-2dserieshausdorff

mia-2dserieshausdorff
Prev	Tools for Myocardial Perfusion Analysis	Next

mia-2dserieshausdorff

Sysnopis:

mia-2dserieshausdorff {-i string} {-r string} [ │ │ │ options │ │ │ - ...]

Description:

Get the per-slice Hausdorff distance of a segmentation with respect to a given reference segmentation set.

Options:

-i, --in-file=(required, input); string: input segmentation set
-r, --ref-file=(required, input); string: reference segmentation set
-k, --skip=0; int: skip images at the beginning

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the per-frame Hausdorff distance of the segmentations of set segment.set with respect to the segmentation set reference.set skipping two images at the beginning.

mia-2dserieshausdorff  -i segment.set -r reference.set -k 2

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dseriesgradvariation	Home	mia-2dseriessmoothgradMAD

│ │ │ + ...]

Description:

Get the per-slice Hausdorff distance of a segmentation with respect to a given reference segmentation set.

Options:

-i, --in-file=(input, required); string: input segmentation set
-r, --ref-file=(input, required); string: reference segmentation set
-k, --skip=0; int: skip images at the beginning

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the per-frame Hausdorff distance of the segmentations of set segment.set with respect to the segmentation set reference.set skipping two images at the beginning.

mia-2dserieshausdorff  -i segment.set -r reference.set -k 2

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dseriesgradvariation	Home	mia-2dseriessmoothgradMAD

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dseriesmincorr.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-2dseries-mincorr

mia-2dseries-mincorr
Prev	Tools for Myocardial Perfusion Analysis	Next

mia-2dseries-mincorr

Sysnopis:

mia-2dseries-mincorr {-i string} {-o io} [ │ │ │ options │ │ │ - ...]

Description:

Given a set of images of temporal sucession, this program evaluates the minimal correlation of the time-intensity curve between neighboring pixels.

Options:

-i, --in-set=(required, input); string: input segmentation set
-o, --out-set=(required, output); io: output image of minimal correlation. For supported file types see Plugin type: 2dimage/io
-k, --skip=2; ulong: skip images at beginning of series

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the minimal correlation image of a series givemn in segment.set and store the image in OpenEXR format. Skip two images at the beginning of the series.

mia-2dseries-mincorr -i segment.set -o mincorr.exr -k 2

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dsegshiftperslice	Home	mia-2dseries-sectionmask

│ │ │ + ...]

Description:

Given a set of images of temporal sucession, this program evaluates the minimal correlation of the time-intensity curve between neighboring pixels.

Options:

-i, --in-set=(input, required); string: input segmentation set
-o, --out-set=(output, required); io: output image of minimal correlation. For supported file types see Plugin type: 2dimage/io
-k, --skip=2; ulong: skip images at beginning of series

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the minimal correlation image of a series givemn in segment.set and store the image in OpenEXR format. Skip two images at the beginning of the series.

mia-2dseries-mincorr -i segment.set -o mincorr.exr -k 2

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dsegshiftperslice	Home	mia-2dseries-sectionmask

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dseriessectionmask.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-2dseries-sectionmask

mia-2dseries-sectionmask
Prev	Tools for Myocardial Perfusion Analysis	Next

mia-2dseries-sectionmask

Sysnopis:

mia-2dseries-sectionmask {-i string} {-o io} [ │ │ │ options │ │ │ - ...]

Description:

Evaluate the masks for the sections of a segmented frame.

Options:

-i, --in-file=(required, input); string: input segmentation set
-o, --out-file=(required, output); io: output image containing the mask. For supported file types see Plugin type: 2dimage/io
-f, --frame=0; ulong: Frame number for which to extract the mask

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the mask image from the segmentation of image 20 in segment.set and store it to mask20.png:

mia-2dseries-sectionmask -i segment.set -f 20 -o mask20.png

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dseries-mincorr	Home	mia-2dseries-segdistance

│ │ │ + ...]

Description:

Evaluate the masks for the sections of a segmented frame.

Options:

-i, --in-file=(input, required); string: input segmentation set
-o, --out-file=(output, required); io: output image containing the mask. For supported file types see Plugin type: 2dimage/io
-f, --frame=0; ulong: Frame number for which to extract the mask

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the mask image from the segmentation of image 20 in segment.set and store it to mask20.png:

mia-2dseries-sectionmask -i segment.set -f 20 -o mask20.png

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dseries-mincorr	Home	mia-2dseries-segdistance

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dseriessegdistance.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-2dseries-segdistance

mia-2dseries-segdistance
Prev	Tools for Myocardial Perfusion Analysis	Next

mia-2dseries-segdistance

Sysnopis:

mia-2dseries-segdistance {-i string} [ │ │ │ options │ │ │ - ...]

Description:

Get the mean distance of a segmentation boundary to the reference boundary.

Options:

-i, --in-file=(required, input); string: input segmentation set
-r, --reference=20; ulong: reference frame
-k, --skip=0; int: skip images at the beginning

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the mean absolute border distanceof the segmentations of set segment.set with respect to the segmentation given in frame 20.

mia-2dseries-segdistance  -i segment.set -r 20

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dseries-sectionmask	Home	mia-2dseries2dordermedian

│ │ │ + ...]

Description:

Get the mean distance of a segmentation boundary to the reference boundary.

Options:

-i, --in-file=(input, required); string: input segmentation set
-r, --reference=20; ulong: reference frame
-k, --skip=0; int: skip images at the beginning

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the mean absolute border distanceof the segmentations of set segment.set with respect to the segmentation given in frame 20.

mia-2dseries-segdistance  -i segment.set -r 20

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dseries-sectionmask	Home	mia-2dseries2dordermedian

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dseriessmoothgradMAD.html │ │ │ @@ -1,7 +1,7 @@ │ │ │ mia-2dseriessmoothgradMAD

mia-2dseriessmoothgradMAD
Prev	Tools for Myocardial Perfusion Analysis	Next

mia-2dseriessmoothgradMAD

Sysnopis:

mia-2dseriessmoothgradMAD {-i string} {-o io} [ │ │ │ options │ │ │ ...] [ │ │ │ │ │ │ Plugin type: 2dimage/filter │ │ │ │ │ │ - ...]

Description:

Given a set of images of temporal sucession, evaluate the temporal pixel-wise gaussian and evaluate pixel-wise its MAD.A spacial pre-filtering may be applied by specifying additional plugins (filter/2dimage)

Options:

-i, --in-file=(required, input); string: input segmentation set
-o, --out-file=(required, output); io: output file name. For supported file types see Plugin type: 2dimage/io
-k, --skip=0; ulong: Skip files at the beginning
-e, --enlarge-boundary=5; ulong: Enlarge cropbox by number of pixels
-c, --crop: crop image before running statistics
-g, --gauss=1; ulong: gauss filter width for moothing the gradient

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the MAD-image of the bounding box surrounding the segmentation from a series segment.set after applying a temporal Gaussian filter of width 5. No spacial filtering will be applied. The bounding box will be enlarged by 3 pixels in all directions. Store the image in OpenEXR format.

mia-2dseriessmoothgradMAD -i segment.set -o mad.exr -g 2 -c -e 3

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dserieshausdorff	Home	mia-2dseriestovolume

│ │ │ + ...]

Description:

Options:

-i, --in-file=(input, required); string: input segmentation set
-o, --out-file=(output, required); io: output file name. For supported file types see Plugin type: 2dimage/io
-k, --skip=0; ulong: Skip files at the beginning
-e, --enlarge-boundary=5; ulong: Enlarge cropbox by number of pixels
-c, --crop: crop image before running statistics
-g, --gauss=1; ulong: gauss filter width for moothing the gradient

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

mia-2dseriessmoothgradMAD -i segment.set -o mad.exr -g 2 -c -e 3

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dserieshausdorff	Home	mia-2dseriestovolume

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dseriestovolume.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-2dseriestovolume

mia-2dseriestovolume
Prev	Tools for Myocardial Perfusion Analysis	Next

mia-2dseriestovolume

Sysnopis:

mia-2dseriestovolume {-i string} {-o io} [ │ │ │ options │ │ │ - ...]

Description:

Obtaines a 3D volume image by combining the images of the segmentation set.

Options:

-i, --in-file=(required, input); string: input segmentation set
-o, --out-file=(required, output); io: output 3D image . For supported file types see Plugin type: 3dimage/io
-k, --skip=0; ulong: number of frames to skip at the beginning of the series.

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Create the volume volume.v from the series series.set but skip the first two images.

mia-2dseriestovolume -i series.set -k 2 -o volume.v

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dseriessmoothgradMAD	Home	Processing of series of 2D images in a 3D fashion (out-of-core)

│ │ │ + ...]

Description:

Obtaines a 3D volume image by combining the images of the segmentation set.

Options:

-i, --in-file=(input, required); string: input segmentation set
-o, --out-file=(output, required); io: output 3D image . For supported file types see Plugin type: 3dimage/io
-k, --skip=0; ulong: number of frames to skip at the beginning of the series.

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Create the volume volume.v from the series series.set but skip the first two images.

mia-2dseriestovolume -i series.set -k 2 -o volume.v

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dseriessmoothgradMAD	Home	Processing of series of 2D images in a 3D fashion (out-of-core)

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dstackcmeanspresegment.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-2dstack-cmeans-presegment

mia-2dstack-cmeans-presegment
Prev	Processing of series of 2D images in a 3D fashion (out-of-core)	Next

mia-2dstack-cmeans-presegment

Sysnopis:

mia-2dstack-cmeans-presegment {-i io} {-o string} {-L int} [ │ │ │ options │ │ │ - ...]

Description:

This program first evaluates a sparse histogram of an input image series, then runs a c-means classification over the histogram, and then estimates the mask for one (given) class based on class probabilities. This program accepts only images of eight or 16 bit integer pixels.

Options:

File-IO

-i, --in-file=(required, input); io: input image(s) to be filtered. For supported file types see Plugin type: 2dimage/io
-p, --out-probmap=(output); string: Save probability map to this file
-t, --type=png; stringSTRING: output file name type
-o, --out-mask=(required, output); string: output file name base

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Parameters

-T, --histogram-thresh=5; float in [0, 50]: Percent of the extrem parts of the histogram to be collapsed into the respective last histogram bin.
-C, --classes=kmeans:nc=3; factory: C-means class initializer. For supported plug-ins see Plugin type: 1d/cmeans
-S, --seed-threshold=0.95; float in (0, 1): Probability threshold value to consider a pixel as seed pixel.
-L, --label=(required); int in [0, 10]: Class label to create the mask from

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run the program over images imageXXXX.png with the sparse histogram, threshold the lower 30% bins (if available), run cmeans with two classes on the non-zero pixels and then create the mask for class 1 as foregroundXXXX.png.

mia-2dstack-cmeans-presegment -i imageXXXX.png -o foreground -t png --histogram-tresh=30 --classes 2 --label 1

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dimagestack-cmeans	Home	mia-2dstackfilter

│ │ │ + ...]

Description:

Options:

File-IO

-i, --in-file=(input, required); io: input image(s) to be filtered. For supported file types see Plugin type: 2dimage/io
-p, --out-probmap=(output); string: Save probability map to this file
-t, --type=png; stringSTRING: output file name type
-o, --out-mask=(output, required); string: output file name base

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Parameters

-T, --histogram-thresh=5; float in [0, 50]: Percent of the extrem parts of the histogram to be collapsed into the respective last histogram bin.
-C, --classes=kmeans:nc=3; factory: C-means class initializer. For supported plug-ins see Plugin type: 1d/cmeans
-S, --seed-threshold=0.95; float in (0, 1): Probability threshold value to consider a pixel as seed pixel.
-L, --label=(required); int in [0, 10]: Class label to create the mask from

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

mia-2dstack-cmeans-presegment -i imageXXXX.png -o foreground -t png --histogram-tresh=30 --classes 2 --label 1

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dimagestack-cmeans	Home	mia-2dstackfilter

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dstackfilter.html │ │ │ @@ -1,7 +1,7 @@ │ │ │ mia-2dstackfilter

mia-2dstackfilter
Prev	Processing of series of 2D images in a 3D fashion (out-of-core)	Next

mia-2dstackfilter

Sysnopis:

mia-2dstackfilter {-i io} {-o io} {-t set} [ │ │ │ options │ │ │ ...] [ │ │ │ │ │ │ Plugin type: 2dstack/filter │ │ │ │ │ │ - ...]

Description:

This program is used to filter and convert a series of 2D gray scale images in a 3D fashion by running filters (filter/2dimage) as given on the command line.

Options:

-i, --in-file=(required, input); io: input image(s) to be filtered. For supported file types see Plugin type: 2dimage/io
-o, --out-file=(required, output); io: output file name base, the actual names is created by adding the file number based on output order and the extension bysed on the 'type' parameter. For supported file types see Plugin type: 2dimage/io
-t, --type=(required); set: output file type Supported values are:(-, @, BMP, DCM, EXR, JPEG, JPG, PNG, RAW, TIF, TIFF, V, VISTA, bmp, dcm, exr, jpeg, jpg, png, raw, tif, tiff, v, vista, )

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run a mean-least-varaiance filter on a series of images that follow the numbering pattern imageXXXX.exr and store the output in images filteredXXXX.exr

mia-2dstackfilter -i image0000.exr -o filtered -t exr mlv:w=2

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dstack-cmeans-presegment	Home	mia-3ddistance

│ │ │ + ...]

Description:

This program is used to filter and convert a series of 2D gray scale images in a 3D fashion by running filters (filter/2dimage) as given on the command line.

Options:

-i, --in-file=(input, required); io: input image(s) to be filtered. For supported file types see Plugin type: 2dimage/io
-o, --out-file=(output, required); io: output file name base, the actual names is created by adding the file number based on output order and the extension bysed on the 'type' parameter. For supported file types see Plugin type: 2dimage/io
-t, --type=(required); set: output file type Supported values are:(-, @, BMP, DCM, EXR, JPEG, JPG, PNG, RAW, TIF, TIFF, V, VISTA, bmp, dcm, exr, jpeg, jpg, png, raw, tif, tiff, v, vista, )

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run a mean-least-varaiance filter on a series of images that follow the numbering pattern imageXXXX.exr and store the output in images filteredXXXX.exr

mia-2dstackfilter -i image0000.exr -o filtered -t exr mlv:w=2

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dstack-cmeans-presegment	Home	mia-3ddistance

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dto3dimage.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-2dto3dimage

mia-2dto3dimage
Prev	Image conversion	Next

mia-2dto3dimage

Sysnopis:

mia-2dto3dimage {-i io} {-o io} [ │ │ │ options │ │ │ - ...]

Description:

This program is used to combine a series of 2D images of equal size and type images following a certain numbering scheme to a 3D image.

Options:

-i, --in-file=(required, input); io: input image(s) to be combined. For supported file types see Plugin type: 2dimage/io
-o, --out-file=(required, output); io: output file name. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Convert a series of images imageXXXX.png to a 3D image 3d.v

mia-2dto3dimage -i imageXXXX.png -o 3d.v

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dmultiimageto3d	Home	mia-2dto3dimageb

│ │ │ + ...]

Description:

This program is used to combine a series of 2D images of equal size and type images following a certain numbering scheme to a 3D image.

Options:

-i, --in-file=(input, required); io: input image(s) to be combined. For supported file types see Plugin type: 2dimage/io
-o, --out-file=(output, required); io: output file name. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Convert a series of images imageXXXX.png to a 3D image 3d.v

mia-2dto3dimage -i imageXXXX.png -o 3d.v

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dmultiimageto3d	Home	mia-2dto3dimageb

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dto3dimageb.html │ │ │ @@ -1,7 +1,7 @@ │ │ │ mia-2dto3dimageb

mia-2dto3dimageb
Prev	Image conversion	Next

mia-2dto3dimageb

Sysnopis:

mia-2dto3dimageb {-o io} [ │ │ │ options │ │ │ ...] [ │ │ │ │ │ │ Plugin type: 2dimage/io │ │ │ │ │ │ - ...]

Description:

This program is used to convert a series 2D images into a 3D image. The 2D images are read as additional command line parameters and the slice ordering corresponds to the ordering of the file names on the commend line.

Options:

-o, --out-file=(required, output); io: output file name. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Convert a series of images imageXXXX.png to a 3D image 3d.v

mia-2dto3dimageb -i imageXXXX.png -o 3d.v

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dto3dimage	Home	mia-3dgetslice

│ │ │ + ...]

Description:

Options:

-o, --out-file=(output, required); io: output file name. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Convert a series of images imageXXXX.png to a 3D image 3d.v

mia-2dto3dimageb -i imageXXXX.png -o 3d.v

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dto3dimage	Home	mia-3dgetslice

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dtrackpixelmovement.html │ │ │ @@ -1,8 +1,8 @@ │ │ │ mia-2dtrackpixelmovement

mia-2dtrackpixelmovement
Prev	Tools for the Analysis of 2D image series	Next

mia-2dtrackpixelmovement

Sysnopis:

mia-2dtrackpixelmovement {-i string} {-o string} {-t io} [ │ │ │ options │ │ │ ...]

Description:

Track the position of a pixel by means of a transformation obtained by using image registration. The pixel data is given in CSV format │ │ │ id;time;x;y;z;reserved │ │ │ │ │ │ The fields 'time', 'x', 'y', and 'z' are updated, and the fields 'id' and 'reserved' are preserved, empty lines are ignored.

Options:

│ │ │ -File-IO

-i, --in-file=(required, input); string: input point set
-o, --out-file=(required, output); string: output point set
-t, --transformation=(required, input); io: transformation describing the monitored change. For supported file types see Plugin type: 2dtransform/io

│ │ │ +File-IO

-i, --in-file=(input, required); string: input point set
-o, --out-file=(output, required); string: output point set
-t, --transformation=(input, required); io: transformation describing the monitored change. For supported file types see Plugin type: 2dtransform/io

│ │ │ Parameters

-T, --time-step=1; float: time step to use for the position update

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

This program evaluated the changed position of pixels given in input.csv, by using a time step of 2.0 time units and the transformation change.v2df, and writes the updated positions to updated.csv.

mia-2dtrackpixelmovement -i input.csv -o output.cvs --time-step 2.0 --transformation change.v2df

Author(s):

Gert Wollny

Prev	Up	Next
mia-2deval-transformquantity	Home	Tools for Myocardial Perfusion Analysis

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dtransform.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-2dtransform

mia-2dtransform
Prev	Registration, Comparison, and Transformation of 2D images	Next

mia-2dtransform

Sysnopis:

mia-2dtransform {-i io} {-o io} {-t io} [ │ │ │ options │ │ │ - ...]

Description:

This program is used to deform a 2D image using a given transformation.

Options:

-i, --in-file=(required, input); io: input image. For supported file types see Plugin type: 2dimage/io
-o, --out-file=(required, output); io: output image. For supported file types see Plugin type: 2dimage/io
-t, --transformation=(required, input); io: transformation file name. For supported file types see Plugin type: 2dtransform/io
-p, --interpolator=STRING: override the interpolator provided by the transformation
-b, --boundary=mirror; stringSTRING: override the boundary conditions provided by the transformation. This is only used if the interpolator is overridden.

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Transform an image input.png by the transfromation stored in trans.v by using linear interpolation and zero boundary conditions and store the result in output.png

mia-2dtransform -i input.png -t trans.v  -o output.png  -p bspline:d=1 -b zero

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dmultiimageregistration	Home	mia-2dtransformation-to-strain

│ │ │ + ...]

Description:

This program is used to deform a 2D image using a given transformation.

Options:

-i, --in-file=(input, required); io: input image. For supported file types see Plugin type: 2dimage/io
-o, --out-file=(output, required); io: output image. For supported file types see Plugin type: 2dimage/io
-t, --transformation=(input, required); io: transformation file name. For supported file types see Plugin type: 2dtransform/io
-p, --interpolator=STRING: override the interpolator provided by the transformation
-b, --boundary=mirror; stringSTRING: override the boundary conditions provided by the transformation. This is only used if the interpolator is overridden.

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Transform an image input.png by the transfromation stored in trans.v by using linear interpolation and zero boundary conditions and store the result in output.png

mia-2dtransform -i input.png -t trans.v  -o output.png  -p bspline:d=1 -b zero

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dmultiimageregistration	Home	mia-2dtransformation-to-strain

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dtransformationtostrain.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-2dtransformation-to-strain

mia-2dtransformation-to-strain
Prev	Registration, Comparison, and Transformation of 2D images	Next

mia-2dtransformation-to-strain

Sysnopis:

mia-2dtransformation-to-strain {-i io} {-o string} [ │ │ │ options │ │ │ - ...]

Description:

Evaluate the Green strain tensor corresponding to a given 2D transformation for each grid point.

Options:

-i, --in-file=(required, input); io: input transformation. For supported file types see Plugin type: 2dtransform/io
-o, --out-file=(required, output); string: output Green's strain tensor

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the Green strain tensor from the transformation stored in trans.v and save it to output.v

mia-2dtransformation-to-strain -i  trans.v  -o output.mt

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dtransform	Home	Registration of series of 2D images

│ │ │ + ...]

Description:

Evaluate the Green strain tensor corresponding to a given 2D transformation for each grid point.

Options:

-i, --in-file=(input, required); io: input transformation. For supported file types see Plugin type: 2dtransform/io
-o, --out-file=(output, required); string: output Green's strain tensor

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the Green strain tensor from the transformation stored in trans.v and save it to output.v

mia-2dtransformation-to-strain -i  trans.v  -o output.mt

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dtransform	Home	Registration of series of 2D images

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dbinarycombine.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-3dbinarycombine

mia-3dbinarycombine
Prev	Analysis, filtering, combining, and segmentation of 3D images	Next

mia-3dbinarycombine

Sysnopis:

mia-3dbinarycombine {-1 io} {-2 io} {-o io} [ │ │ │ options │ │ │ - ...]

Description:

This program is used to combine two binary images by some kind of operation.

Options:

-1, --file1=(required, input); io

input mask image 1. For supported file types see Plugin type: 3dimage/io

-2, --file2=(required, input); io

input mask image 2. For supported file types see Plugin type: 3dimage/io

-p, --operation=nor; dict

Operation to be applied

or:	logocal or
nor:	logocal nor
and:	logocal and
nand:	logocal nand
xor:	logocal xor
nxor:	logocal nxor

-o, --out-file=(required, output); io

output mask image. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Combine the binary images b1.png and b2.png by using the 'nor' operation and store the result in b1nor2.png.

mia-3dbinarycombine -1 b1.png -2 b2.png -p nor -o b1nor2.png

Author(s):

Gert Wollny

Prev	Up	Next
Analysis, filtering, combining, and segmentation of 3D images	Home	mia-3dbrainextractT1

│ │ │ + ...]

Description:

This program is used to combine two binary images by some kind of operation.

Options:

-1, --file1=(input, required); io

input mask image 1. For supported file types see Plugin type: 3dimage/io

-2, --file2=(input, required); io

input mask image 2. For supported file types see Plugin type: 3dimage/io

-p, --operation=nor; dict

Operation to be applied

or:	logocal or
nor:	logocal nor
and:	logocal and
nand:	logocal nand
xor:	logocal xor
nxor:	logocal nxor

-o, --out-file=(output, required); io

output mask image. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Combine the binary images b1.png and b2.png by using the 'nor' operation and store the result in b1nor2.png.

mia-3dbinarycombine -1 b1.png -2 b2.png -p nor -o b1nor2.png

Author(s):

Gert Wollny

Prev	Up	Next
Analysis, filtering, combining, and segmentation of 3D images	Home	mia-3dbrainextractT1

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dbrainextractT1.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-3dbrainextractT1

mia-3dbrainextractT1
Prev	Analysis, filtering, combining, and segmentation of 3D images	Next

mia-3dbrainextractT1

Sysnopis:

mia-3dbrainextractT1 {-i io} {-o io} [ │ │ │ options │ │ │ - ...]

Description:

This program is used to extract the brain from T1 MR images. It first runs a combined fuzzy c-means clustering and B-field correction to facilitate a 3D segmentation of 3D image. Then various fiters are run to obtain a white matter segmentation as initial mask that is then used to run a region growing to obtain a mask of the whole brain. Finally, this mask is used to extact the brain from the B0 field corrected images.

Options:

-i, --in-file=(required, input); io: input image(s) to be segmented. For supported file types see Plugin type: 3dimage/io
-o, --out-file=(required, output); io: brain mask. For supported file types see Plugin type: 3dimage/io
-n, --no-of-classes=3; int: number of classes
-w, --wm-class=2; int: index of white matter
-p, --wm-prob=0.7; float: white matter class probability for initial mask creation
-t, --grow-threshold=20; int: intensity threshold for region growing
--grow-shape=18n; stringSTRING: neighbourhood mask region growing

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Create a mask from the input image by running a 5-class segmentation over inpt image input.v and use class 4 as white matter class and store the masked image in masked.v and the B0-field corrected image in b0.v

mia-3dbrainextractT1 -i input.v -n 5 -w 4 -o masked.v

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dbinarycombine	Home	mia-3dcombine-imageseries

│ │ │ + ...]

Description:

Options:

-i, --in-file=(input, required); io: input image(s) to be segmented. For supported file types see Plugin type: 3dimage/io
-o, --out-file=(output, required); io: brain mask. For supported file types see Plugin type: 3dimage/io
-n, --no-of-classes=3; int: number of classes
-w, --wm-class=2; int: index of white matter
-p, --wm-prob=0.7; float: white matter class probability for initial mask creation
-t, --grow-threshold=20; int: intensity threshold for region growing
--grow-shape=18n; stringSTRING: neighbourhood mask region growing

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

mia-3dbrainextractT1 -i input.v -n 5 -w 4 -o masked.v

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dbinarycombine	Home	mia-3dcombine-imageseries

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dcombineimageseries.html │ │ │ @@ -1,8 +1,8 @@ │ │ │ mia-3dcombine-imageseries

mia-3dcombine-imageseries
Prev	Analysis, filtering, combining, and segmentation of 3D images	Next

mia-3dcombine-imageseries

Sysnopis:

mia-3dcombine-imageseries {-o io} [ │ │ │ options │ │ │ ...] [ │ │ │ │ │ │ Plugin type: 3dimage/io │ │ │ │ │ │ - ...]

Description:

This programs takes various input images of the same dimensions and creates a combined output images that uses the define operation for the combination.

Options:

-o, --out-file=(required, output); io

output file that contains the combined image.. For supported file types see Plugin type: 3dimage/io

-p, --operation=mean; dict

Operation to be applied when combining the images

mean:	mean image intensities
max:	select max per pixel intensity
add:	add pixel intensities

-r, --repn=none; dict

Output pixel representation (if not given, then the representation of the first input image will be used

bit:	binary data
sbyte:	signed 8 bit
ubyte:	unsigned 8 bit
sshort:	signed 16 bit
ushort:	unsigned 16 bit
sint:	signed 32 bit
uint:	unsigned 32 bit
slong:	signed 64 bit
ulong:	unsigned 64 bit
float:	floating point 32 bit
double:	floating point 64 bit
none:	no pixel type defined

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

│ │ │ + ...]

Description:

This programs takes various input images of the same dimensions and creates a combined output images that uses the define operation for the combination.

Options:

-o, --out-file=(output, required); io

output file that contains the combined image.. For supported file types see Plugin type: 3dimage/io

-p, --operation=mean; dict

Operation to be applied when combining the images

mean:	mean image intensities
max:	select max per pixel intensity
add:	add pixel intensities

-r, --repn=none; dict

Output pixel representation (if not given, then the representation of the first input image will be used

bit:	binary data
sbyte:	signed 8 bit
ubyte:	unsigned 8 bit
sshort:	signed 16 bit
ushort:	unsigned 16 bit
sint:	signed 32 bit
uint:	unsigned 32 bit
slong:	signed 64 bit
ulong:	unsigned 64 bit
float:	floating point 32 bit
double:	floating point 64 bit
none:	no pixel type defined

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

│ │ │

mia-3dcombine-imageseries

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dbrainextractT1	Home	mia-3dcombine-mr-segmentations

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dcombinemrsegmentations.html │ │ │ @@ -1,8 +1,8 @@ │ │ │ mia-3dcombine-mr-segmentations

mia-3dcombine-mr-segmentations
Prev	Analysis, filtering, combining, and segmentation of 3D images	Next

mia-3dcombine-mr-segmentations

Sysnopis:

mia-3dcombine-mr-segmentations {-i io} {-o io} [ │ │ │ options │ │ │ ...] [ │ │ │ │ │ │ Plugin type: 3dimage/io │ │ │ │ │ │ - ...]

Description:

This programs takes various segmentation masks of the same data and a tissue probability image set and combines them into one labeled image. The masks are translated to labels according to the position on the command line. If a voxel is set as belonging to more then one mask, the probabilities are consulted.

Options:

-i, --in-file=(required, input); io: input probability images. The number of mask images must correspond to the number of probability images given here.. For supported file types see Plugin type: 3dimage/io
-o, --out-file=(required, output); io: output image that contains the labeling.. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

│ │ │ + ...]

Description:

Options:

-i, --in-file=(input, required); io: input probability images. The number of mask images must correspond to the number of probability images given here.. For supported file types see Plugin type: 3dimage/io
-o, --out-file=(output, required); io: output image that contains the labeling.. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

│ │ │

mia-3dcombine-mr-segmentations

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dcombine-imageseries	Home	mia-3dcrispsegment

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dcosttranslatedgrad.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-3dcost-translatedgrad

mia-3dcost-translatedgrad
Prev	Registration, Comparison, and Transformation of 3D images	Next

mia-3dcost-translatedgrad

Sysnopis:

mia-3dcost-translatedgrad {-i io} {-r io} {-o io} [ │ │ │ options │ │ │ - ...]

Description:

Evaluate the cost gradient between two images and evaluate the transformation related gradient for it based on the given transformation model.

Options:

-i, --in-file=(required, input); io: input image . For supported file types see Plugin type: 3dimage/io
-r, --ref-file=(required, input); io: reference image . For supported file types see Plugin type: 3dimage/io
-o, --out-file=(required, output); io: output vector field . For supported file types see Plugin type: 3dtransform/io
-g, --gradimg-file=(output); io: norm image of the spline transformed gradient. For supported file types see Plugin type: 3dimage/io
-C, --cost-gradimg-file=(output); io: norm image of the cost gradient. For supported file types see Plugin type: 3dimage/io
-f, --transForm=spline:rate=5; factory: Transformation the gradient relates to. For supported plug-ins see Plugin type: 3dimage/transform
-c, --cost=ssd; factory: cost function to use. For supported plug-ins see Plugin type: 3dimage/cost

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the SSD cost between src.v and ref.v and store the gradient gradient corresponding to a spline transformation in grad.v3dt.

mia-3dcost-translatedgrad -i src.v -o grad.v3dt -f spline:rate=8 -c ssd

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dcost	Home	mia-3ddeform

│ │ │ + ...]

Description:

Evaluate the cost gradient between two images and evaluate the transformation related gradient for it based on the given transformation model.

Options:

-i, --in-file=(input, required); io: input image . For supported file types see Plugin type: 3dimage/io
-r, --ref-file=(input, required); io: reference image . For supported file types see Plugin type: 3dimage/io
-o, --out-file=(output, required); io: output vector field . For supported file types see Plugin type: 3dtransform/io
-g, --gradimg-file=(output); io: norm image of the spline transformed gradient. For supported file types see Plugin type: 3dimage/io
-C, --cost-gradimg-file=(output); io: norm image of the cost gradient. For supported file types see Plugin type: 3dimage/io
-f, --transForm=spline:rate=5; factory: Transformation the gradient relates to. For supported plug-ins see Plugin type: 3dimage/transform
-c, --cost=ssd; factory: cost function to use. For supported plug-ins see Plugin type: 3dimage/cost

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the SSD cost between src.v and ref.v and store the gradient gradient corresponding to a spline transformation in grad.v3dt.

mia-3dcost-translatedgrad -i src.v -o grad.v3dt -f spline:rate=8 -c ssd

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dcost	Home	mia-3ddeform

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dcrispsegment.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-3dcrispsegment

mia-3dcrispsegment
Prev	Analysis, filtering, combining, and segmentation of 3D images	Next

mia-3dcrispsegment

Sysnopis:

mia-3dcrispsegment {-i io} {-o io} [ │ │ │ options │ │ │ - ...]

Description:

This program creates a label image from a fuzzy segmentation. or each pixel the label is set to the class with the higest probability plus a given offset

Options:

-i, --in-file=(required, input); io: input class file, should contain multiple images with tissue class probabilities. For supported file types see Plugin type: 3dimage/io
-o, --out-file=(required, output); io: output class label image. For supported file types see Plugin type: 3dimage/io
-l, --label-offset=1; uint: label offset

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Set the labels based on the input class probability file cls.v adding the offset 2 to each label and save the result to labeled.v.

mia-3dcrispsegment -i cls.v -o labeled.v -l 2

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dcombine-mr-segmentations	Home	mia-3ddistance-stats

│ │ │ + ...]

Description:

This program creates a label image from a fuzzy segmentation. or each pixel the label is set to the class with the higest probability plus a given offset

Options:

-i, --in-file=(input, required); io: input class file, should contain multiple images with tissue class probabilities. For supported file types see Plugin type: 3dimage/io
-o, --out-file=(output, required); io: output class label image. For supported file types see Plugin type: 3dimage/io
-l, --label-offset=1; uint: label offset

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Set the labels based on the input class probability file cls.v adding the offset 2 to each label and save the result to labeled.v.

mia-3dcrispsegment -i cls.v -o labeled.v -l 2

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dcombine-mr-segmentations	Home	mia-3ddistance-stats

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3ddeform.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-3ddeform

mia-3ddeform
Prev	Registration, Comparison, and Transformation of 3D images	Next

mia-3ddeform

Sysnopis:

mia-3ddeform {-i io} {-o io} {-t io} [ │ │ │ options │ │ │ - ...]

Description:

Transform a 3D image by applying a given 3D transformation that is defined by a 3D vector field v according to x:=x-v(x)

Options:

-i, --in-image=(required, input); io: input image. For supported file types see Plugin type: 3dimage/io
-o, --out-image=(required, output); io: transformed image. For supported file types see Plugin type: 3dimage/io
-t, --transformation=(required, input); io: transformation vector field. For supported file types see Plugin type: 3dvf/io
-p, --interpolator=bspline:d=3; factory: image interpolator kernel. For supported plug-ins see Plugin type: 1d/splinekernel

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Transform an image input.v by the transformation defined by the vector field field.v by using bspline interpolation of degree 4 and store the result in output.v

mia-3ddeform -i input.v -t field.v  -o output.v  -p bspline:d=4

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dcost-translatedgrad	Home	mia-3dfluid

│ │ │ + ...]

Description:

Transform a 3D image by applying a given 3D transformation that is defined by a 3D vector field v according to x:=x-v(x)

Options:

-i, --in-image=(input, required); io: input image. For supported file types see Plugin type: 3dimage/io
-o, --out-image=(output, required); io: transformed image. For supported file types see Plugin type: 3dimage/io
-t, --transformation=(input, required); io: transformation vector field. For supported file types see Plugin type: 3dvf/io
-p, --interpolator=bspline:d=3; factory: image interpolator kernel. For supported plug-ins see Plugin type: 1d/splinekernel

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Transform an image input.v by the transformation defined by the vector field field.v by using bspline interpolation of degree 4 and store the result in output.v

mia-3ddeform -i input.v -t field.v  -o output.v  -p bspline:d=4

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dcost-translatedgrad	Home	mia-3dfluid

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3ddistance.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-3ddistance

mia-3ddistance
Prev	Processing of series of 2D images in a 3D fashion (out-of-core)	Next

mia-3ddistance

Sysnopis:

mia-3ddistance {-i string} {-r string} {-o string} [ │ │ │ options │ │ │ - ...]

Description:

This program takes two binary masks as input and evaluates the distance of one mask with respect to the other in voxel space. The output is given as text file with the coordinates of the source voxels and their distance to the reference mask. Correction for voxel size must be done after processing.

Options:

File IO

-i, --in-file=(required, input); string: input image(s) that contain the source pixel mask
-r, --ref-file=(required, input); string: reference mask to evaluate the distance from
-o, --out-file=(required, output); string: output file name

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Test

--self-test: run a self test

Example:

Evaluate the distance of the mask given in the images srcXXXX.png to the mask given in refXXXX.png and save the result to distances.txt

mia-3ddistance -i srcXXXX.png -r refXXXX.png -o distances.txt

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dstackfilter	Home	mia-multihist

│ │ │ + ...]

Description:

Options:

File IO

-i, --in-file=(input, required); string: input image(s) that contain the source pixel mask
-r, --ref-file=(input, required); string: reference mask to evaluate the distance from
-o, --out-file=(output, required); string: output file name

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Test

--self-test: run a self test

Example:

Evaluate the distance of the mask given in the images srcXXXX.png to the mask given in refXXXX.png and save the result to distances.txt

mia-3ddistance -i srcXXXX.png -r refXXXX.png -o distances.txt

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dstackfilter	Home	mia-multihist

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3ddistancestats.html │ │ │ @@ -14,8 +14,8 @@ │ │ │ end_range <- 2 + as.numeric(line[2]) │ │ │ s <- as.numeric(line[3:end_range]) │ │ │ result <- sprintf("%d %8.4f %8.4f %8.4f %8.4f\n" │ │ │ label, mean(s), sqrt(var(s)), median(s), max(s)) │ │ │ cat(result) │ │ │ } │ │ │ │ │ │ -

Options:

File-IO

-i, --in-labels=(required, input); io: input label image. For supported file types see Plugin type: 3dimage/io
-r, --ref-labels=(required, input); io: reference label image. For supported file types see Plugin type: 3dimage/io
-l, --label-map=(input); string: optional mapping of label numbers
-o, --out-file=(required, output); string: output file name to write the distances to. The output file is a csv file, containing distances listed for each label.

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the distances for each label available in image.v to the corresponding labels in the image reference.v ans store the result a coma separated list of values, i.e. distances.csv.

mia-3ddistance-stats -i image.v -r reference.v -o distances.csv

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dcrispsegment	Home	mia-3dfuzzysegment

│ │ │ +

Options:

File-IO

-i, --in-labels=(input, required); io: input label image. For supported file types see Plugin type: 3dimage/io
-r, --ref-labels=(input, required); io: reference label image. For supported file types see Plugin type: 3dimage/io
-l, --label-map=(input); string: optional mapping of label numbers
-o, --out-file=(output, required); string: output file name to write the distances to. The output file is a csv file, containing distances listed for each label.

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the distances for each label available in image.v to the corresponding labels in the image reference.v ans store the result a coma separated list of values, i.e. distances.csv.

mia-3ddistance-stats -i image.v -r reference.v -o distances.csv

Author(s):

Gert Wollny

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mia-3dcrispsegment	Home	mia-3dfuzzysegment

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3devaltransformquantity.html │ │ │ @@ -14,9 +14,9 @@ │ │ │ style=sparse #storage style (sparse|grid) │ │ │ repn=float32 #representation of values │ │ │ size=1000 1000 200 #grid size of the transformation │ │ │ endian=low #endianess of binary data (low|big) │ │ │ } │ │ │ │ │ │ This example header has to be interpreted like follows: three-dimensional data, each entry consists of 13 values the values etry consists of a 3D vector, a scalar, and a 3x3 matrix (saved in row-major format).The data records represent strain tensors, and only a sparse set of points is given. The values are given as single floating point (32 bit). The original transformation field corresponds to images of 1000x1000x200 voxels and the binary data is stored in low endian format.

Options:

│ │ │ -File-IO

-i, --in-file=(input); string: input point set, if this parameter is given a sparse evaluation of the quantity will be done, otherwise the quantity is evaluated for each grid point of the transformation range.
-o, --out-file=(required, output); string: output strains file, for a format description see above.
-t, --transformation=(required, input); io: transformation of which the quantity will be evaluated.. For supported file types see Plugin type: 3dtransform/io

│ │ │ +File-IO

-i, --in-file=(input); string: input point set, if this parameter is given a sparse evaluation of the quantity will be done, otherwise the quantity is evaluated for each grid point of the transformation range.
-o, --out-file=(output, required); string: output strains file, for a format description see above.
-t, --transformation=(input, required); io: transformation of which the quantity will be evaluated.. For supported file types see Plugin type: 3dtransform/io

│ │ │ Parameters

-q, --quantity=strain; dict

Specify the quantity to be evaluated at the given points

derivative:	Evaluate the transformation derivative at the given points
strain:	Evaluate the strain tensor at the given points

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Derivative of the transformation change.v3df for each point given in input.csv are evaluated and written to output.s.

mia-3deval-transformquantity -i input.csv -o output.s --transformation change.v3df

Author(s):

Gert Wollny

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Tools for the Analysis of 3D image series	Home	mia-3dseries-track-intensity

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dfield2norm.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-3dfield2norm

mia-3dfield2norm
Prev	Miscellaneous programs	Next

mia-3dfield2norm

Sysnopis:

mia-3dfield2norm {-i io} {-o io} [ │ │ │ options │ │ │ - ...]

Description:

This program converts a 3d vector field to an image of its voxel-wise norm.

Options:

-i, --in-vectorfield=(required, input); io: input vector field. For supported file types see Plugin type: 3dvf/io
-o, --out-image=(required, output); io: output image comprising the per voxel norm of each image. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the norm image norm.v from a vector field field.v.

mia-3dfield2norm -i field.v -o norm.v

Author(s):

Gert Wollny

Prev	Up	Next
Miscellaneous programs	Home	mia-3dimageaddattributes

│ │ │ + ...]

Description:

This program converts a 3d vector field to an image of its voxel-wise norm.

Options:

-i, --in-vectorfield=(input, required); io: input vector field. For supported file types see Plugin type: 3dvf/io
-o, --out-image=(output, required); io: output image comprising the per voxel norm of each image. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the norm image norm.v from a vector field field.v.

mia-3dfield2norm -i field.v -o norm.v

Author(s):

Gert Wollny

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Miscellaneous programs	Home	mia-3dimageaddattributes

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dfluid.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-3dfluid

mia-3dfluid
Prev	Registration, Comparison, and Transformation of 3D images	Next

mia-3dfluid

Sysnopis:

mia-3dfluid {-i io} {-r io} {-o io} [ │ │ │ options │ │ │ - ...]

Description:

This program is used for non-rigid registration based on fluid dynamics as described in:

Wollny, G. and Kruggel, F., 'Computational cost of non-rigid registration algorithms based on fluid dynamics', IEEE Transactions on Medical Imaging, 11(8), pp. 946-952, 2002.

It uses SSD as the sole registration criterion.

Options:

File-IO

-i, --in-image=(required, input); io: input image. For supported file types see Plugin type: 3dimage/io
-r, --ref-image=(required, input); io: reference image . For supported file types see Plugin type: 3dimage/io
-o, --out-transformation=(required, output); io: output transformation comprising the registering transformation field. For supported file types see Plugin type: 3dtransform/io
-d, --out-image=(output); io: save deformed image. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Registration parameters

--disable-multigrid

disable multi-grid processing

--disable-fullres

disable processing on the full resolution image

--lambda=1; float

elasticy constant

--mu=1; float

elasticy constant

-s, --start-size=16; int

initial multigrided size

-m, --method=sora; dict

method for solving PDE

sor:	successive overrelaxation
sora:	Gauss Southwell relexation

--step=0.8; float

Initial stepsize

-p, --interpolator=bspline:d=3; factory

image interpolator kernel. For supported plug-ins see Plugin type: 1d/splinekernel

--relax=1; float

overrelaxation factor vor method sor

--maxiter=10; int

maximum iterations

--epsilon=0.01; float

truncation condition

--matter=4; float

intensity above which real matter is assumed (experimental)

Example:

Register image test.v to image ref.v and write the deformation vector field regfield.v. Start registration at the smallest size above 16 pixel.

mia-3dfluid -i test.v -r ref.v -o regfield.v -s 16

Author(s):

Gert Wollny

Prev	Up	Next
mia-3ddeform	Home	mia-3dfluid-syn-registration

│ │ │ + ...]

Description:

This program is used for non-rigid registration based on fluid dynamics as described in:

Wollny, G. and Kruggel, F., 'Computational cost of non-rigid registration algorithms based on fluid dynamics', IEEE Transactions on Medical Imaging, 11(8), pp. 946-952, 2002.

It uses SSD as the sole registration criterion.

Options:

File-IO

-i, --in-image=(input, required); io: input image. For supported file types see Plugin type: 3dimage/io
-r, --ref-image=(input, required); io: reference image . For supported file types see Plugin type: 3dimage/io
-o, --out-transformation=(output, required); io: output transformation comprising the registering transformation field. For supported file types see Plugin type: 3dtransform/io
-d, --out-image=(output); io: save deformed image. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Registration parameters

--disable-multigrid

disable multi-grid processing

--disable-fullres

disable processing on the full resolution image

--lambda=1; float

elasticy constant

--mu=1; float

elasticy constant

-s, --start-size=16; int

initial multigrided size

-m, --method=sora; dict

method for solving PDE

sor:	successive overrelaxation
sora:	Gauss Southwell relexation

--step=0.8; float

Initial stepsize

-p, --interpolator=bspline:d=3; factory

image interpolator kernel. For supported plug-ins see Plugin type: 1d/splinekernel

--relax=1; float

overrelaxation factor vor method sor

--maxiter=10; int

maximum iterations

--epsilon=0.01; float

truncation condition

--matter=4; float

intensity above which real matter is assumed (experimental)

Example:

Register image test.v to image ref.v and write the deformation vector field regfield.v. Start registration at the smallest size above 16 pixel.

mia-3dfluid -i test.v -r ref.v -o regfield.v -s 16

Author(s):

Gert Wollny

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mia-3ddeform	Home	mia-3dfluid-syn-registration

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dfluidsynregistration.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-3dfluid-syn-registration

mia-3dfluid-syn-registration
Prev	Registration, Comparison, and Transformation of 3D images	Next

mia-3dfluid-syn-registration

Sysnopis:

mia-3dfluid-syn-registration {-i io} {-r io} {-o io} {-O io} [ │ │ │ options │ │ │ - ...]

Description:

This program implements the registration of two gray scale 3D images. The transformation applied is a symmeric diffeomorpic fluid dynamic registration. To work most efficiently, this program makes a few assumptions about the imput data, i.e. the image must be of the same size, have the same voxel spacing, and any intensity range normalization or equalization should also be done before calling this program.

Options:

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

IO

-i, --in-image=(required, input); io: test image. For supported file types see Plugin type: 3dimage/io
-r, --ref-image=(required, input); io: reference image. For supported file types see Plugin type: 3dimage/io
-o, --transform=(required, output); io: output transformation. For supported file types see Plugin type: 3dtransform/io
-O, --inverse-transform=(required, output); io: inverse output transformation. For supported file types see Plugin type: 3dtransform/io

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Registration

-l, --mg-levels=3; uint: Number of multi-resolution levels to run the registration on. Not that some registration parameters can be given as a coma seperated list to indicate per level values. In these cases if the number of given values is smaller than the number of multi-resolution levels (this parameter), the the last given value is used for all subsequest multi-resolution levels.
-S, --step=0.25; float in (0, 0.5]: Initial step size for all levels
-c, --cost=ssd; factory: Image similarity function to be minimized. For supported plug-ins see Plugin type: 3dimage/cost
-R, --regularizer=sor:kernel=fluid,maxiter=50; factory: Regularization for the force to transformation update. For supported plug-ins see Plugin type: 3dvf/regularizer
-T, --conv-test-interval= in [4, 40]: Convergence test interations intervall: In order to measure convergence the cost function value is averaged over this amount of iterations, and the decline rate is evaluated based on the linare regression of the cost function values in this intervall. This parameter can be given as a coma-seperated list with values corresponding to the multi-resolution levels, see option --mg-levels for more information.
-D, --stop-decline-rate= in [0, inf): Stopping criterium for registration based on the cost decline rate. If the rate below this value, the iteration is stopped. This parameter can be given as a coma-seperated list with values corresponding to the multi-resolution levels, see option --mg-levels for more information.
-C, --stop-cost=: Stopping criterium for registration based on the cost value. If the cost drops below this value, the iteration is stopped. This parameter can be given as a coma-seperated list with values corresponding to the multi-resolution levels, see option --mg-levels for more information.
-I, --iter= in [4, inf): Naximum number if iterations done on each multi-resolution level. This parameter can be given as a coma-seperated list with values corresponding to the multi-resolution levels, see option --mg-levels for more information.

Example:

Register image test.v to image ref.v saving the transformation to transform.v and the inverse transform to inverse-transform.v. Use three multiresolution levels, ssd as image cost function.

mia-3dfluid-syn-registration -i test.v -r ref.v -t transform.v -T inverse-transform.v  -l 3 ssd

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dfluid	Home	mia-3dforce

│ │ │ + ...]

Description:

Options:

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

IO

-i, --in-image=(input, required); io: test image. For supported file types see Plugin type: 3dimage/io
-r, --ref-image=(input, required); io: reference image. For supported file types see Plugin type: 3dimage/io
-o, --transform=(output, required); io: output transformation. For supported file types see Plugin type: 3dtransform/io
-O, --inverse-transform=(output, required); io: inverse output transformation. For supported file types see Plugin type: 3dtransform/io

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Registration

-l, --mg-levels=3; uint: Number of multi-resolution levels to run the registration on. Not that some registration parameters can be given as a coma seperated list to indicate per level values. In these cases if the number of given values is smaller than the number of multi-resolution levels (this parameter), the the last given value is used for all subsequest multi-resolution levels.
-S, --step=0.25; float in (0, 0.5]: Initial step size for all levels
-c, --cost=ssd; factory: Image similarity function to be minimized. For supported plug-ins see Plugin type: 3dimage/cost
-R, --regularizer=sor:kernel=fluid,maxiter=50; factory: Regularization for the force to transformation update. For supported plug-ins see Plugin type: 3dvf/regularizer
-T, --conv-test-interval= in [4, 40]: Convergence test interations intervall: In order to measure convergence the cost function value is averaged over this amount of iterations, and the decline rate is evaluated based on the linare regression of the cost function values in this intervall. This parameter can be given as a coma-seperated list with values corresponding to the multi-resolution levels, see option --mg-levels for more information.
-D, --stop-decline-rate= in [0, inf): Stopping criterium for registration based on the cost decline rate. If the rate below this value, the iteration is stopped. This parameter can be given as a coma-seperated list with values corresponding to the multi-resolution levels, see option --mg-levels for more information.
-C, --stop-cost=: Stopping criterium for registration based on the cost value. If the cost drops below this value, the iteration is stopped. This parameter can be given as a coma-seperated list with values corresponding to the multi-resolution levels, see option --mg-levels for more information.
-I, --iter= in [4, inf): Naximum number if iterations done on each multi-resolution level. This parameter can be given as a coma-seperated list with values corresponding to the multi-resolution levels, see option --mg-levels for more information.

Example:

Register image test.v to image ref.v saving the transformation to transform.v and the inverse transform to inverse-transform.v. Use three multiresolution levels, ssd as image cost function.

mia-3dfluid-syn-registration -i test.v -r ref.v -t transform.v -T inverse-transform.v  -l 3 ssd

Author(s):

Gert Wollny

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mia-3dfluid	Home	mia-3dforce

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dforce.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-3dforce

mia-3dforce
Prev	Registration, Comparison, and Transformation of 3D images	Next

mia-3dforce

Sysnopis:

mia-3dforce {-i io} {-r io} {-o io} [ │ │ │ options │ │ │ - ...]

Description:

This program is used to create an image comprising the pixel-wise norm of the ggradient of a given cost function.

Options:

-i, --src-file=(required, input); io: input image. For supported file types see Plugin type: 3dimage/io
-r, --ref-file=(required, input); io: output force norm image. For supported file types see Plugin type: 3dimage/io
-o, --out-file=(required, output); io: reference image. For supported file types see Plugin type: 3dimage/io
-c, --cost=ssd; factory: cost function to use. For supported plug-ins see Plugin type: 3dimage/cost

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the weigtes sum of SSD between src.v and ref.v and store the result in forcenorm.v.

mia-3dforce -i src.v -r ref.v -c ssd -o forcenorm.v

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dfluid-syn-registration	Home	mia-3dlandmarks-distances

│ │ │ + ...]

Description:

This program is used to create an image comprising the pixel-wise norm of the ggradient of a given cost function.

Options:

-i, --src-file=(input, required); io: input image. For supported file types see Plugin type: 3dimage/io
-r, --ref-file=(input, required); io: output force norm image. For supported file types see Plugin type: 3dimage/io
-o, --out-file=(output, required); io: reference image. For supported file types see Plugin type: 3dimage/io
-c, --cost=ssd; factory: cost function to use. For supported plug-ins see Plugin type: 3dimage/cost

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the weigtes sum of SSD between src.v and ref.v and store the result in forcenorm.v.

mia-3dforce -i src.v -r ref.v -c ssd -o forcenorm.v

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dfluid-syn-registration	Home	mia-3dlandmarks-distances

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dfuzzysegment.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-3dfuzzysegment

mia-3dfuzzysegment
Prev	Analysis, filtering, combining, and segmentation of 3D images	Next

mia-3dfuzzysegment

Sysnopis:

mia-3dfuzzysegment {-i io} [ │ │ │ options │ │ │ - ...]

Description:

This program runs a combined fuzzy c-means clustering and B-field correction to facilitate a 3D segmentation of 3D image

Options:

-i, --in-file=(required, input); io: input image(s) to be segmenetd. For supported file types see Plugin type: 3dimage/io
-c, --cls-file=(output); io: output class probability images. Note, the used file format must support multible images (best is to use vista). For supported file types see Plugin type: 3dimage/io
-o, --b0-file=(output); io: image corrected for intensity non-uniformity. For supported file types see Plugin type: 3dimage/io
-n, --no-of-classes=3; int: number of classes
-r, --residuum=0.1; float: relative residuum

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run a 5-class segmentation over inpt image input.v and store the class probability images in cls.v and the B0-field corrected image in b0.v.

mia-3dfuzzysegment -i input.v -c 5 -o b0.v -c cls.v

Author(s):

Gert Wollny

Prev	Up	Next
mia-3ddistance-stats	Home	mia-3dgetsize

│ │ │ + ...]

Description:

This program runs a combined fuzzy c-means clustering and B-field correction to facilitate a 3D segmentation of 3D image

Options:

-i, --in-file=(input, required); io: input image(s) to be segmenetd. For supported file types see Plugin type: 3dimage/io
-c, --cls-file=(output); io: output class probability images. Note, the used file format must support multible images (best is to use vista). For supported file types see Plugin type: 3dimage/io
-o, --b0-file=(output); io: image corrected for intensity non-uniformity. For supported file types see Plugin type: 3dimage/io
-n, --no-of-classes=3; int: number of classes
-r, --residuum=0.1; float: relative residuum

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run a 5-class segmentation over inpt image input.v and store the class probability images in cls.v and the B0-field corrected image in b0.v.

mia-3dfuzzysegment -i input.v -c 5 -o b0.v -c cls.v

Author(s):

Gert Wollny

Prev	Up	Next
mia-3ddistance-stats	Home	mia-3dgetsize

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dgetsize.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-3dgetsize

mia-3dgetsize
Prev	Analysis, filtering, combining, and segmentation of 3D images	Next

mia-3dgetsize

Sysnopis:

mia-3dgetsize {-i io} [ │ │ │ options │ │ │ - ...]

Description:

Write the dimensions of the input 3D image to stdout.

Options:

-i, --in-file=(required, input); io: input image(s) to be filtered. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Print out the size of image.v.

mia-3dgetsize -i image.v

Author(s):

Gert Wollny

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mia-3dfuzzysegment	Home	mia-3dimagecombine

│ │ │ + ...]

Description:

Write the dimensions of the input 3D image to stdout.

Options:

-i, --in-file=(input, required); io: input image(s) to be filtered. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Print out the size of image.v.

mia-3dgetsize -i image.v

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dfuzzysegment	Home	mia-3dimagecombine

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dgetslice.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-3dgetslice

mia-3dgetslice
Prev	Image conversion	Next

mia-3dgetslice

Sysnopis:

mia-3dgetslice {-i io} {-o io} [ │ │ │ options │ │ │ - ...]

Description:

This program is used to extract 2D slices from a 3D data set and store them in separate files. Output files will be numbered according to their slice index.

Options:

-i, --in-file=(required, input); io

input image(s) to be filtered. For supported file types see Plugin type: 3dimage/io

-o, --out-file=(required, output); io

output image(s). If number != 1 than this is used as a base name and should be given without extension since this will be based on the '--type' option. If number=1 then this exact file name will be used.. For supported file types see Plugin type: 2dimage/io

-t, --type=png; set

output file type for number != 1 Supported values are:(bmp, datapool, dicom, exr, jpg, png, raw, tif, vista, )

-s, --start=0; ulong

start slice number

-n, --number=1; ulong

number of slices (all=0)

--ndigits=4; int

minimum number of digits of the file name numbers (if n != 1)

-d, --dir=xy; dict

slice direction (xy=axial, xz=coronal, yz=saggital)

xy:	get xy (axial) slice
xz:	get xz (coronal) slice
yz:	get yz (saggital) slice

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Store 5 coronal slices starting at slice 120 coronalXXXX.png from image.v.

mia-3dgetslice -i image.v -o coronal -t png -n 5 -s 120

Author(s):

Gert Wollny

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mia-2dto3dimageb	Home	mia-3dimageselect

│ │ │ + ...]

Description:

This program is used to extract 2D slices from a 3D data set and store them in separate files. Output files will be numbered according to their slice index.

Options:

-i, --in-file=(input, required); io

input image(s) to be filtered. For supported file types see Plugin type: 3dimage/io

-o, --out-file=(output, required); io

-t, --type=png; set

output file type for number != 1 Supported values are:(bmp, datapool, dicom, exr, jpg, png, raw, tif, vista, )

-s, --start=0; ulong

start slice number

-n, --number=1; ulong

number of slices (all=0)

--ndigits=4; int

minimum number of digits of the file name numbers (if n != 1)

-d, --dir=xy; dict

slice direction (xy=axial, xz=coronal, yz=saggital)

xy:	get xy (axial) slice
xz:	get xz (coronal) slice
yz:	get yz (saggital) slice

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Store 5 coronal slices starting at slice 120 coronalXXXX.png from image.v.

mia-3dgetslice -i image.v -o coronal -t png -n 5 -s 120

Author(s):

Gert Wollny

Prev	Up	Next
mia-2dto3dimageb	Home	mia-3dimageselect

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dimageaddattributes.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-3dimageaddattributes

mia-3dimageaddattributes
Prev	Miscellaneous programs	Next

mia-3dimageaddattributes

Sysnopis:

mia-3dimageaddattributes {-i io} {-o io} {-a io} [ │ │ │ options │ │ │ - ...]

Description:

This program appends all the meta-data attributes found in a 2D input image to a 3D image (if the output format supports such attributes). Attributes that are already present in the 3D image are not overwritten.

Options:

-i, --in-file=(required, input); io: input image(s) to be filtered. For supported file types see Plugin type: 3dimage/io
-o, --out-file=(required, output); io: output image(s) with the added attributes. For supported file types see Plugin type: 3dimage/io
-a, --attr=(required, input); io: 2D image providing the attributes. For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Append the attributes found in 2d.v to 3d.v and store the result in attr3d.v

mia-3dimageaddattributes  -i 3d.v -o attr3d.v -a 2d.v

Author(s):

Gert Wollny

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mia-3dfield2norm	Home	mia-3dvectorfieldcreate

│ │ │ + ...]

Description:

Options:

-i, --in-file=(input, required); io: input image(s) to be filtered. For supported file types see Plugin type: 3dimage/io
-o, --out-file=(output, required); io: output image(s) with the added attributes. For supported file types see Plugin type: 3dimage/io
-a, --attr=(input, required); io: 2D image providing the attributes. For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Append the attributes found in 2d.v to 3d.v and store the result in attr3d.v

mia-3dimageaddattributes  -i 3d.v -o attr3d.v -a 2d.v

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dfield2norm	Home	mia-3dvectorfieldcreate

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dimagecombine.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-3dimagecombine

mia-3dimagecombine
Prev	Analysis, filtering, combining, and segmentation of 3D images	Next

mia-3dimagecombine

Sysnopis:

mia-3dimagecombine {-1 io} {-2 io} {-c factory} {-o io} [ │ │ │ options │ │ │ - ...]

Description:

This program is used to combine two images using a given image combiner.

Options:

-1, --image1=(required, input); io: input image 1 to be combined. For supported file types see Plugin type: 3dimage/io
-2, --image2=(required, input); io: input image 2 to be combined. For supported file types see Plugin type: 3dimage/io
-c, --combiner=(required); factory: combiner operation. For supported plug-ins see Plugin type: 3dimage/combiner
-o, --out-file=(required, output); io: output image file. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Take two images l1.v and l2.v and evaluate the per-voxel sum.

mia-3dimagecombine -1 l1.v -2 l2.v -c sum.v -c add

Author(s):

Gert Wollny

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mia-3dgetsize	Home	mia-3dimagecreator

│ │ │ + ...]

Description:

This program is used to combine two images using a given image combiner.

Options:

-1, --image1=(input, required); io: input image 1 to be combined. For supported file types see Plugin type: 3dimage/io
-2, --image2=(input, required); io: input image 2 to be combined. For supported file types see Plugin type: 3dimage/io
-c, --combiner=(required); factory: combiner operation. For supported plug-ins see Plugin type: 3dimage/combiner
-o, --out-file=(output, required); io: output image file. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Take two images l1.v and l2.v and evaluate the per-voxel sum.

mia-3dimagecombine -1 l1.v -2 l2.v -c sum.v -c add

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dgetsize	Home	mia-3dimagecreator

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dimagecreator.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-3dimagecreator

mia-3dimagecreator
Prev	Analysis, filtering, combining, and segmentation of 3D images	Next

mia-3dimagecreator

Sysnopis:

mia-3dimagecreator {-o io} [ │ │ │ options │ │ │ - ...]

Description:

This program creates a 3D image that contains an object created by one of the object creator plug-ins (creator/3dimage)

Options:

-o, --out-file=(required, output); io

output file for create object. For supported file types see Plugin type: 3dimage/io

-s, --size=[128,128,128]; 3dbounds

size of the object

-r, --repn=ubyte; dict

input pixel type

bit:	binary data
sbyte:	signed 8 bit
ubyte:	unsigned 8 bit
sshort:	signed 16 bit
ushort:	unsigned 16 bit
sint:	signed 32 bit
uint:	unsigned 32 bit
slong:	signed 64 bit
ulong:	unsigned 64 bit
float:	floating point 32 bit
double:	floating point 64 bit
none:	no pixel type defined

-j, --object=sphere; factory

object to be created. For supported plug-ins see Plugin type: 3dimage/creator

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Create an image output.v of size <64,128,256> that contains a lattic with frequencys 8, 16, and 4 in x, y and, z-direction respectively.

mia-3dimagecreator -o lattic.v -j lattic:fx=8,fy=16,fz=4 -s "<64,128,256>"

Author(s):

Gert Wollny

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mia-3dimagecombine	Home	mia-3dimagefilter

│ │ │ + ...]

Description:

This program creates a 3D image that contains an object created by one of the object creator plug-ins (creator/3dimage)

Options:

-o, --out-file=(output, required); io

output file for create object. For supported file types see Plugin type: 3dimage/io

-s, --size=[128,128,128]; 3dbounds

size of the object

-r, --repn=ubyte; dict

input pixel type

bit:	binary data
sbyte:	signed 8 bit
ubyte:	unsigned 8 bit
sshort:	signed 16 bit
ushort:	unsigned 16 bit
sint:	signed 32 bit
uint:	unsigned 32 bit
slong:	signed 64 bit
ulong:	unsigned 64 bit
float:	floating point 32 bit
double:	floating point 64 bit
none:	no pixel type defined

-j, --object=sphere; factory

object to be created. For supported plug-ins see Plugin type: 3dimage/creator

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Create an image output.v of size <64,128,256> that contains a lattic with frequencys 8, 16, and 4 in x, y and, z-direction respectively.

mia-3dimagecreator -o lattic.v -j lattic:fx=8,fy=16,fz=4 -s "<64,128,256>"

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dimagecombine	Home	mia-3dimagefilter

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dimagefilter.html │ │ │ @@ -1,7 +1,7 @@ │ │ │ mia-3dimagefilter

mia-3dimagefilter
Prev	Analysis, filtering, combining, and segmentation of 3D images	Next

mia-3dimagefilter

Sysnopis:

mia-3dimagefilter {-i io} {-o io} [ │ │ │ options │ │ │ ...] [ │ │ │ │ │ │ Plugin type: 3dimage/filter │ │ │ │ │ │ - ...]

Description:

This program is used to filter and convert gray scale 3D images.

Options:

-i, --in-file=(required, input); io: input image(s) to be filtered. For supported file types see Plugin type: 3dimage/io
-o, --out-file=(required, output); io: output image(s) that have been filtered. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run a mean-least-varaiance filter on input.v, then run a 5-class k-means classification and binarize by selecting the 4th class.

mia-3dimagefilter -i image.v -o filtered.v mlv:w=2 kmeans:c=5 binarize:min=4,max=4

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dimagecreator	Home	mia-3dimagefilterstack

│ │ │ + ...]

Description:

This program is used to filter and convert gray scale 3D images.

Options:

-i, --in-file=(input, required); io: input image(s) to be filtered. For supported file types see Plugin type: 3dimage/io
-o, --out-file=(output, required); io: output image(s) that have been filtered. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run a mean-least-varaiance filter on input.v, then run a 5-class k-means classification and binarize by selecting the 4th class.

mia-3dimagefilter -i image.v -o filtered.v mlv:w=2 kmeans:c=5 binarize:min=4,max=4

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dimagecreator	Home	mia-3dimagefilterstack

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dimagefilterstack.html │ │ │ @@ -1,7 +1,7 @@ │ │ │ mia-3dimagefilterstack

mia-3dimagefilterstack
Prev	Analysis, filtering, combining, and segmentation of 3D images	Next

mia-3dimagefilterstack

Sysnopis:

mia-3dimagefilterstack {-i io} {-o io} {-t set} [ │ │ │ options │ │ │ ...] [ │ │ │ │ │ │ Plugin type: 3dimage/filter │ │ │ │ │ │ - ...]

Description:

This program is used to filter and convert a consecutive numbered series gray of scale images. File names must follow the pattern 'dataXXXX.v' (X being digits), i.e. the numbering comes right before the dot.

Options:

-i, --in-file=(required, input); io: input image(s) to be filtered. For supported file types see Plugin type: 3dimage/io
-o, --out-file=(required, output); io: output file name base, numbers are added accorfing to the input file pattern, and the file extension is added according to the 'type' option.. For supported file types see Plugin type: 3dimage/io
-t, --type=(required); set: output file type Supported values are:(analyze, datapool, dicom, hdf5, inria, mhd, nifti, vff, vista, vti, vtk, )

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run a mean-least-varaiance filter on a series of images that follow the numbering pattern imageXXXX.hdr and store the output in images filteredXXXX.hdr

mia-3dimagefilterstack -i image0000.hdr -o filtered -t hdr mlv:w=2

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dimagefilter	Home	mia-3dimagestatistics-in-mask

│ │ │ + ...]

Description:

Options:

-i, --in-file=(input, required); io: input image(s) to be filtered. For supported file types see Plugin type: 3dimage/io
-o, --out-file=(output, required); io: output file name base, numbers are added accorfing to the input file pattern, and the file extension is added according to the 'type' option.. For supported file types see Plugin type: 3dimage/io
-t, --type=(required); set: output file type Supported values are:(analyze, datapool, dicom, hdf5, inria, mhd, nifti, vff, vista, vti, vtk, )

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run a mean-least-varaiance filter on a series of images that follow the numbering pattern imageXXXX.hdr and store the output in images filteredXXXX.hdr

mia-3dimagefilterstack -i image0000.hdr -o filtered -t hdr mlv:w=2

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dimagefilter	Home	mia-3dimagestatistics-in-mask

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dimageselect.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-3dimageselect

mia-3dimageselect
Prev	Image conversion	Next

mia-3dimageselect

Sysnopis:

mia-3dimageselect {-i io} {-o io} [ │ │ │ options │ │ │ - ...]

Description:

This program is used to select one 3D images from a multi-image file.

Options:

-i, --in-file=(required, input); io: input images. For supported file types see Plugin type: 3dimage/io
-o, --out-file=(required, output); io: output image. For supported file types see Plugin type: 3dimage/io
-n, --number=0; ulong: image number to be selected

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Store the third image in multiimage.v to image.v (note: counting starts with zero).

mia-3dimageselect -i multiimage.v -o image.v -n 2

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dgetslice	Home	mia-raw2image

│ │ │ + ...]

Description:

This program is used to select one 3D images from a multi-image file.

Options:

-i, --in-file=(input, required); io: input images. For supported file types see Plugin type: 3dimage/io
-o, --out-file=(output, required); io: output image. For supported file types see Plugin type: 3dimage/io
-n, --number=0; ulong: image number to be selected

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Store the third image in multiimage.v to image.v (note: counting starts with zero).

mia-3dimageselect -i multiimage.v -o image.v -n 2

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dgetslice	Home	mia-raw2image

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dimagestatisticsinmask.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-3dimagestatistics-in-mask

mia-3dimagestatistics-in-mask
Prev	Analysis, filtering, combining, and segmentation of 3D images	Next

mia-3dimagestatistics-in-mask

Sysnopis:

mia-3dimagestatistics-in-mask {-i io} {-m io} [ │ │ │ options │ │ │ - ...]

Description:

This program evaluates the statistics of an image within a masked region of the image. Possible outputs are a summary statistics and a histogram of the values.

Options:

File-IO

-i, --image=(required, input); io: input image to be analyzed. For supported file types see Plugin type: 3dimage/io
-m, --mask=(required, input); io: mask image to use to restrict the analysis. For supported file types see Plugin type: 3dimage/io
-s, --summary=(output); string: File to write the summary statistics to as plain text.
-H, --histogram=(output); string: File to write the histogram to

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Parameters

--struct-name=undefined; stringSTRING: Name of the structure the statistics are evaluated for
-l, --limit=20; uint in [20, inf): Number of pixels the mask should at least contain.
-b, --bins=8; ulong in [4, inf): number of histogram bins to be used
--hmin=0; float: lower bound for the histogram mapping. All values below this value will be mapped into the lowest bin. If this parameter is equal or larger than hmax, the histogram range is evaluated automatically.
--hmax=0; float: hpper bound for the histogram mapping. All values above this valuewill be mapped into the highest bin. If this parameter is equal or smaller than hmin, the histogram range is evaluated automatically.

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

evaluate the summary statistics on the input and a histogram with 10 bins and automtically evaluated boundaries. Save summary in summary.txt and the histogram in hist.txt

mia-3dimagestatistics-in-mask --image image.v.gz --mask mask.v.gz --summary summary.txt --histogram hist.txt

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dimagefilterstack	Home	mia-3dimagestats

│ │ │ + ...]

Description:

This program evaluates the statistics of an image within a masked region of the image. Possible outputs are a summary statistics and a histogram of the values.

Options:

File-IO

-i, --image=(input, required); io: input image to be analyzed. For supported file types see Plugin type: 3dimage/io
-m, --mask=(input, required); io: mask image to use to restrict the analysis. For supported file types see Plugin type: 3dimage/io
-s, --summary=(output); string: File to write the summary statistics to as plain text.
-H, --histogram=(output); string: File to write the histogram to

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Parameters

--struct-name=undefined; stringSTRING: Name of the structure the statistics are evaluated for
-l, --limit=20; uint in [20, inf): Number of pixels the mask should at least contain.
-b, --bins=8; ulong in [4, inf): number of histogram bins to be used
--hmin=0; float: lower bound for the histogram mapping. All values below this value will be mapped into the lowest bin. If this parameter is equal or larger than hmax, the histogram range is evaluated automatically.
--hmax=0; float: hpper bound for the histogram mapping. All values above this valuewill be mapped into the highest bin. If this parameter is equal or smaller than hmin, the histogram range is evaluated automatically.

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

evaluate the summary statistics on the input and a histogram with 10 bins and automtically evaluated boundaries. Save summary in summary.txt and the histogram in hist.txt

mia-3dimagestatistics-in-mask --image image.v.gz --mask mask.v.gz --summary summary.txt --histogram hist.txt

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dimagefilterstack	Home	mia-3dimagestats

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dimagestats.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-3dimagestats

mia-3dimagestats
Prev	Analysis, filtering, combining, and segmentation of 3D images	Next

mia-3dimagestats

Sysnopis:

mia-3dimagestats {-i io} [ │ │ │ options │ │ │ - ...]

Description:

This program is used to evaluate certain image statistics and print them out on the console.

Options:

-i, --in-file=(required, input); io: input image(s) to be filtered. For supported file types see Plugin type: 3dimage/io
-t, --thresh=10; float: intensity thresh to ignore

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the statistics of image input.v and ignore all voxels with an intensity below 5.

mia-3dimagestats -i input.v -t 5

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dimagestatistics-in-mask	Home	mia-3disosurface-from-stack

│ │ │ + ...]

Description:

This program is used to evaluate certain image statistics and print them out on the console.

Options:

-i, --in-file=(input, required); io: input image(s) to be filtered. For supported file types see Plugin type: 3dimage/io
-t, --thresh=10; float: intensity thresh to ignore

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the statistics of image input.v and ignore all voxels with an intensity below 5.

mia-3dimagestats -i input.v -t 5

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dimagestatistics-in-mask	Home	mia-3disosurface-from-stack

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3disosurfacefromstack.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-3disosurface-from-stack

mia-3disosurface-from-stack
Prev	Analysis, filtering, combining, and segmentation of 3D images	Next

mia-3disosurface-from-stack

Sysnopis:

mia-3disosurface-from-stack {-i string} {-o string} [ │ │ │ options │ │ │ - ...]

Description:

This program is used to extract an iso-surface from the input gray scale image given as slices.

Options:

File-IO

-i, --in-image=(required, input); string: input image filename pattern
-o, --out-mesh=(required, output); string: output mesh

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Image options

-s, --iso-value=128; float: iso-value of iso surface to be extracted

Mesh options

-f, --max-faces=-1; int: maximum number of Faces,
-e, --max-edges=-1; int: maximum number of Edges
-c, --max-cost=0.1; float: maximum cost for edge collaps
-r, --ratio=4; float: ratio of faces(edges) to target number, at which the optimization changes from edge-length to volume-optimized
-w, --reverse-winding: reverse the winding of the triangles in order to make normals point away from the high intensity area

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Extract the surface from an image set with numbers imageXXXX.png that corresponds to the value 30 and stop optimizing when the mesh consists of less than 100000 triangles.

mia-3disosurface-from-stack -i image0000.png -o mesh.vmesh -s 30 -f 100000

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dimagestats	Home	mia-3dlerp

│ │ │ + ...]

Description:

This program is used to extract an iso-surface from the input gray scale image given as slices.

Options:

File-IO

-i, --in-image=(input, required); string: input image filename pattern
-o, --out-mesh=(output, required); string: output mesh

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Image options

-s, --iso-value=128; float: iso-value of iso surface to be extracted

Mesh options

-f, --max-faces=-1; int: maximum number of Faces,
-e, --max-edges=-1; int: maximum number of Edges
-c, --max-cost=0.1; float: maximum cost for edge collaps
-r, --ratio=4; float: ratio of faces(edges) to target number, at which the optimization changes from edge-length to volume-optimized
-w, --reverse-winding: reverse the winding of the triangles in order to make normals point away from the high intensity area

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Extract the surface from an image set with numbers imageXXXX.png that corresponds to the value 30 and stop optimizing when the mesh consists of less than 100000 triangles.

mia-3disosurface-from-stack -i image0000.png -o mesh.vmesh -s 30 -f 100000

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dimagestats	Home	mia-3dlerp

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3disosurfacefromvolume.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-3disosurface-from-volume

mia-3disosurface-from-volume
Prev	Creation, analysis, and filtering of triangular 3D meshes	Next

mia-3disosurface-from-volume

Sysnopis:

mia-3disosurface-from-volume {-i io} {-o io} [ │ │ │ options │ │ │ - ...]

Description:

This program is used to extract an iso-surface from the input gray scale image by using marching thetrahedra.

Options:

File-IO

-i, --in-file=(required, input); io: input image. For supported file types see Plugin type: 3dimage/io
-o, --out-file=(required, output); io: output mesh. For supported file types see Plugin type: mesh/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Image options

-s, --iso-value=128; float: iso-value of iso surface to be extracted
-b, --bordered: put an empty border around the image to ensure a closed surface

Mesh options

-f, --max-faces=-1; int: maximum number of Faces,
-e, --max-edges=-1; int: maximum number of Edges
-c, --max-cost=0.1; float: maximum cost for edge collaps
-r, --ratio=4; float: ratio of faces(edges) to target number, at which the optimization changes from edge-length to volume-optimized
-w, --reverse-winding: reverse the winding of the triangles in order to make normals point away from the high intensity area

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Extract the surface corresponding to the value 30 and stop optimizing when the mesh consists of less than 100000 triangles.

mia-3disosurface-from-volume -i image.v -o mesh.vmesh -s 30 -f 100000

Author(s):

Gert Wollny

Prev	Up	Next
Creation, analysis, and filtering of triangular 3D meshes	Home	mia-mesh-deformable-model

│ │ │ + ...]

Description:

This program is used to extract an iso-surface from the input gray scale image by using marching thetrahedra.

Options:

File-IO

-i, --in-file=(input, required); io: input image. For supported file types see Plugin type: 3dimage/io
-o, --out-file=(output, required); io: output mesh. For supported file types see Plugin type: mesh/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Image options

-s, --iso-value=128; float: iso-value of iso surface to be extracted
-b, --bordered: put an empty border around the image to ensure a closed surface

Mesh options

-f, --max-faces=-1; int: maximum number of Faces,
-e, --max-edges=-1; int: maximum number of Edges
-c, --max-cost=0.1; float: maximum cost for edge collaps
-r, --ratio=4; float: ratio of faces(edges) to target number, at which the optimization changes from edge-length to volume-optimized
-w, --reverse-winding: reverse the winding of the triangles in order to make normals point away from the high intensity area

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Extract the surface corresponding to the value 30 and stop optimizing when the mesh consists of less than 100000 triangles.

mia-3disosurface-from-volume -i image.v -o mesh.vmesh -s 30 -f 100000

Author(s):

Gert Wollny

Prev	Up	Next
Creation, analysis, and filtering of triangular 3D meshes	Home	mia-mesh-deformable-model

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dlandmarksdistances.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-3dlandmarks-distances

mia-3dlandmarks-distances
Prev	Registration, Comparison, and Transformation of 3D images	Next

mia-3dlandmarks-distances

Sysnopis:

mia-3dlandmarks-distances {-i io} {-o io} [ │ │ │ options │ │ │ - ...]

Description:

Evaluate Euclidian distances between the corresponding landmarks in two landmark sets. The programs prints out only values for landmarks that are available and have location values in both sets

Options:

-i, --in-file-1=(required, input); io: input landmark set 1. For supported file types see Plugin type: 3dlandmarklist/io
-o, --in-file-2=(required, input); io: input landmark set 2. For supported file types see Plugin type: 3dlandmarklist/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the distance between the landmarks in set input1.lmx and input2.lmx and write the result to stdout

mia-3dlandmarks-distances -1 input1.lmx -2 input2.v

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dforce	Home	mia-3dlandmarks-transform

│ │ │ + ...]

Description:

Evaluate Euclidian distances between the corresponding landmarks in two landmark sets. The programs prints out only values for landmarks that are available and have location values in both sets

Options:

-i, --in-file-1=(input, required); io: input landmark set 1. For supported file types see Plugin type: 3dlandmarklist/io
-o, --in-file-2=(input, required); io: input landmark set 2. For supported file types see Plugin type: 3dlandmarklist/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the distance between the landmarks in set input1.lmx and input2.lmx and write the result to stdout

mia-3dlandmarks-distances -1 input1.lmx -2 input2.v

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dforce	Home	mia-3dlandmarks-transform

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dlandmarkstransform.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-3dlandmarks-transform

mia-3dlandmarks-transform
Prev	Registration, Comparison, and Transformation of 3D images	Next

mia-3dlandmarks-transform

Sysnopis:

mia-3dlandmarks-transform {-i io} {-o io} {-t io} [ │ │ │ options │ │ │ - ...]

Description:

Transform the locations of the landmarks by means of a given 3D transformation. Note, landmark transformations do the inverse of an image transformation (in a manner of speaking), i.e. given a transformation V(x) in an image transformation the pixel intensity at x is set to the original intensity at V(x), while a landmark at x is moved to V(x).

Options:

-i, --in-file=(required, input); io: input landmark set. For supported file types see Plugin type: 3dlandmarklist/io
-o, --out-file=(required, output); io: output landmark set. For supported file types see Plugin type: 3dlandmarklist/io
-t, --transformation=(required, input); io: transformation file. For supported file types see Plugin type: 3dtransform/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Transform the landmarks given in input.lmx by applyning the transfromation stored in trans.v and store the result in output.lmx

mia-3dlandmarks-transform -i input.lmx -t trans.v  -o output.lmx

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dlandmarks-distances	Home	mia-3dnonrigidreg

│ │ │ + ...]

Description:

Options:

-i, --in-file=(input, required); io: input landmark set. For supported file types see Plugin type: 3dlandmarklist/io
-o, --out-file=(output, required); io: output landmark set. For supported file types see Plugin type: 3dlandmarklist/io
-t, --transformation=(input, required); io: transformation file. For supported file types see Plugin type: 3dtransform/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Transform the landmarks given in input.lmx by applyning the transfromation stored in trans.v and store the result in output.lmx

mia-3dlandmarks-transform -i input.lmx -t trans.v  -o output.lmx

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dlandmarks-distances	Home	mia-3dnonrigidreg

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dlerp.html │ │ │ @@ -1,7 +1,7 @@ │ │ │ mia-3dlerp

mia-3dlerp
Prev	Analysis, filtering, combining, and segmentation of 3D images	Next

mia-3dlerp

Sysnopis:

mia-3dlerp {-1 io} {-2 io} {-o io} {-p vfloat} [ │ │ │ options │ │ │ - ...]

Description:

merge two images by linear combination.

Options:

-1, --first=(required, input); io: first input image . For supported file types see Plugin type: 3dimage/io
-2, --second=(required, input); io: second input image . For supported file types see Plugin type: 3dimage/io
-o, --out-file=(required, output); io: linearly interpolated image. For supported file types see Plugin type: 3dimage/io
-p, --positions=(required); vfloat: image series positions (first, target, second)

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Test

--selftest=(: run a self test of the program

Example:

Combine image inputA.v and inputB.v by using position coordinates 4, 7, and 9. This means the output pixel values will be evaluated according to │ │ │ + ...]

Description:

merge two images by linear combination.

Options:

-1, --first=(input, required); io: first input image . For supported file types see Plugin type: 3dimage/io
-2, --second=(input, required); io: second input image . For supported file types see Plugin type: 3dimage/io
-o, --out-file=(output, required); io: linearly interpolated image. For supported file types see Plugin type: 3dimage/io
-p, --positions=(required); vfloat: image series positions (first, target, second)

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Test

--selftest=(: run a self test of the program

Example:

mia-3dlerp -1 inputA.v -2 inputB.v -p 4,7,9 -o output.v

Author(s):

Gert Wollny

Prev	Up	Next
mia-3disosurface-from-stack	Home	mia-3dmaskseeded

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dmany2onenonrigid.html │ │ │ @@ -1,9 +1,9 @@ │ │ │ mia-3dmany2one-nonrigid

mia-3dmany2one-nonrigid
Prev	Registration of series of 3D images	Next

mia-3dmany2one-nonrigid

Sysnopis:

mia-3dmany2one-nonrigid {-i io} [ │ │ │ options │ │ │ ...] [ │ │ │ │ │ │ Plugin type: 3dimage/fullcost │ │ │ │ │ │ ...]

Description:

This program runs the non-rigid registration of an image series by registereing all images to a user-selected reference.

Options:

│ │ │ -File-IO

-i, --in-file=(required, input); io: input perfusion data set. For supported file types see Plugin type: 3dimage/io
-o, --out-file=(output); io: file name for registered files. For supported file types see Plugin type: 3dimage/io

│ │ │ +File-IO

-i, --in-file=(input, required); io: input perfusion data set. For supported file types see Plugin type: 3dimage/io
-o, --out-file=(output); io: file name for registered files. For supported file types see Plugin type: 3dimage/io

│ │ │ Registration

-O, --optimizer=gsl:opt=gd,step=0.1; stringSTRING: Optimizer used for minimization
-l, --mg-levels=3; ulong: multi-resolution levels
-f, --transForm=spline; factory: transformation type. For supported plug-ins see Plugin type: 3dimage/transform
-r, --ref=-1; int: reference frame (-1 == use image in the middle)

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Register the images given as numbered files imagesXXXX.v by optimizing a spline based transformation with a coefficient rate of 16 pixel using a weighted combination of normalized gradient fields and SSD as cost measure, and penalize the transformation by using divcurl with aweight of 2.0. Store the resultsing images in registeredXXXX.v.

mia-3dmany2one-nonrigid -i images0000.v -o  registered%04d.v -F spline:rate=16 image:cost=[ngf:eval=ds],weight=2.0 image:cost=ssd,weight=0.1 divcurl:weight=2.0

Author(s):

Gert Wollny

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Registration of series of 3D images	Home	mia-3dmotioncompica-nonrigid

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dmaskseeded.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-3dmaskseeded

mia-3dmaskseeded
Prev	Analysis, filtering, combining, and segmentation of 3D images	Next

mia-3dmaskseeded

Sysnopis:

mia-3dmaskseeded {-i io} {-o io} [ │ │ │ options │ │ │ - ...]

Description:

3D image segmentation based on region growing from a seed point. Neighboring points are added, either when their intensity is equal or higher than that of the seed point, or of the intensity is lower or equal then that of the neighoring point. After region growing is finished, this mask is used to zero out the region in the original image yielding the resulting image.

Options:

-i, --in-file=(required, input); io: input image(s) to be filtered. For supported file types see Plugin type: 3dimage/io
-o, --out-file=(required, output); io: output image(s) that have been filtered. For supported file types see Plugin type: 3dimage/io
-s, --seed=[0,0,0]; 3dbounds: seed point
-n, --neighborhood=6n; factory: neighborhood shape. For supported plug-ins see Plugin type: 3dimage/shape

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run a region growing on input.v starting at point <10,23,21> and use the 18n neighbourhood.

mia-3dmaskseeded -i image.v -o masked.v -s '<10,23,21>' -n 18n

Author(s):

Gert Wollny

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mia-3dlerp	Home	mia-3dpropose-boundingbox

│ │ │ + ...]

Description:

Options:

-i, --in-file=(input, required); io: input image(s) to be filtered. For supported file types see Plugin type: 3dimage/io
-o, --out-file=(output, required); io: output image(s) that have been filtered. For supported file types see Plugin type: 3dimage/io
-s, --seed=[0,0,0]; 3dbounds: seed point
-n, --neighborhood=6n; factory: neighborhood shape. For supported plug-ins see Plugin type: 3dimage/shape

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run a region growing on input.v starting at point <10,23,21> and use the 18n neighbourhood.

mia-3dmaskseeded -i image.v -o masked.v -s '<10,23,21>' -n 18n

Author(s):

Gert Wollny

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mia-3dlerp	Home	mia-3dpropose-boundingbox

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dmotioncompicanonrigid.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-3dmotioncompica-nonrigid

mia-3dmotioncompica-nonrigid
Prev	Registration of series of 3D images	Next

mia-3dmotioncompica-nonrigid

Sysnopis:

mia-3dmotioncompica-nonrigid {-i io} {-o io} [ │ │ │ options │ │ │ - ...]

Description:

This program implements a 3D version of the motion compensation algorithm described in

Options:

File-IO

-i, --in-file=(required, input); io: input images of consecutively numbered filed (nameXXXX.ext). For supported file types see Plugin type: 3dimage/io
-o, --out-file=(required, output); io: output image name (as C format string including a %04d in order to define the file numbering). For supported file types see Plugin type: 3dimage/io
--save-refs=STRING: save reference images, the given string is used as file name base, the number pattern follows the input images, and the output format is always 'vista'
--save-regs=STRING: save intermediate registered images, the given string is used as file name base, the number pattern follows the input images, and the output format is always 'vista'
--save-coeffs=STRING: save mixing matrix to a text file
--save-features=STRING: save feature images as PNG

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

ICA

--fastica=internal; factory: FastICA implementationto be used. For supported plug-ins see Plugin type: fastica/implementation
-C, --components=0; ulong: ICA components 0 = automatic estimation
--no-normalize: don't normalized ICs
--no-meanstrip: don't strip the mean from the mixing curves
-k, --skip=0; ulong: skip images at the beginning of the series e.g. because as they are of other modalities
-m, --max-ica-iter=400; ulong: maximum number of iterations in ICA

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Registration

-O, --optimizer=gsl:opt=gd,step=0.1; stringSTRING: Optimizer used for minimization
-a, --start-c-rate=32; double: start coefficinet rate in spines, gets divided by --c-rate-divider with every pass
--c-rate-divider=4; double: cofficient rate divider for each pass
-d, --start-divcurl=20; double: start divcurl weight, gets divided by --divcurl-divider with every pass
--divcurl-divider=4; double: divcurl weight scaling with each new pass
-w, --imagecost=image:weight=1,cost=ssd,; stringSTRING: image cost
-l, --mg-levels=3; ulong: multi-resolution levels
-P, --passes=3; ulong: registration passes

Example:

Register the perfusion series given in images imagesXXXX.v by using 4-class ICA estimation. Skip two images at the beginning, use at most 4 registration threads, a nlopt based optimizer and otherwiese use the default parameters. Store the result in registeredXXXX.v

mia-3dmotioncompica-nonrigid -i images0000.v -o  registered%04d.v  -k 2 -C 4 -t 4 -O nlopt:opt=ld-var1,xtola=0.001,ftolr=0.001,maxiter=300

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dmany2one-nonrigid	Home	mia-3dprealign-nonrigid

│ │ │ + ...]

Description:

This program implements a 3D version of the motion compensation algorithm described in

Options:

File-IO

-i, --in-file=(input, required); io: input images of consecutively numbered filed (nameXXXX.ext). For supported file types see Plugin type: 3dimage/io
-o, --out-file=(output, required); io: output image name (as C format string including a %04d in order to define the file numbering). For supported file types see Plugin type: 3dimage/io
--save-refs=STRING: save reference images, the given string is used as file name base, the number pattern follows the input images, and the output format is always 'vista'
--save-regs=STRING: save intermediate registered images, the given string is used as file name base, the number pattern follows the input images, and the output format is always 'vista'
--save-coeffs=STRING: save mixing matrix to a text file
--save-features=STRING: save feature images as PNG

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

ICA

--fastica=internal; factory: FastICA implementationto be used. For supported plug-ins see Plugin type: fastica/implementation
-C, --components=0; ulong: ICA components 0 = automatic estimation
--no-normalize: don't normalized ICs
--no-meanstrip: don't strip the mean from the mixing curves
-k, --skip=0; ulong: skip images at the beginning of the series e.g. because as they are of other modalities
-m, --max-ica-iter=400; ulong: maximum number of iterations in ICA

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Registration

-O, --optimizer=gsl:opt=gd,step=0.1; stringSTRING: Optimizer used for minimization
-a, --start-c-rate=32; double: start coefficinet rate in spines, gets divided by --c-rate-divider with every pass
--c-rate-divider=4; double: cofficient rate divider for each pass
-d, --start-divcurl=20; double: start divcurl weight, gets divided by --divcurl-divider with every pass
--divcurl-divider=4; double: divcurl weight scaling with each new pass
-w, --imagecost=image:weight=1,cost=ssd,; stringSTRING: image cost
-l, --mg-levels=3; ulong: multi-resolution levels
-P, --passes=3; ulong: registration passes

Example:

mia-3dmotioncompica-nonrigid -i images0000.v -o  registered%04d.v  -k 2 -C 4 -t 4 -O nlopt:opt=ld-var1,xtola=0.001,ftolr=0.001,maxiter=300

Author(s):

Gert Wollny

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mia-3dmany2one-nonrigid	Home	mia-3dprealign-nonrigid

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dnonrigidreg.html │ │ │ @@ -1,7 +1,7 @@ │ │ │ mia-3dnonrigidreg

mia-3dnonrigidreg
Prev	Registration, Comparison, and Transformation of 3D images	Next

mia-3dnonrigidreg

Sysnopis:

mia-3dnonrigidreg {-i io} {-r io} {-o io} [ │ │ │ options │ │ │ ...] [ │ │ │ │ │ │ Plugin type: 3dimage/fullcost │ │ │ │ │ │ - ...]

Description:

This program implements the registration of two gray scale 3D images.

Options:

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

IO

-i, --in-image=(required, input); io: test image. For supported file types see Plugin type: 3dimage/io
-r, --ref-image=(required, input); io: reference image. For supported file types see Plugin type: 3dimage/io
-o, --out-image=(required, output); io: registered output image. For supported file types see Plugin type: 3dimage/io
-t, --transformation=(output); io: output transformation. For supported file types see Plugin type: 3dtransform/io

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Registration

-l, --levels=3; ulong: multi-resolution levels
-O, --optimizer=gsl:opt=gd,step=0.1; factory: Optimizer used for minimization. For supported plug-ins see Plugin type: minimizer/singlecost
-f, --transForm=spline:rate=10; factory: transformation type. For supported plug-ins see Plugin type: 3dimage/transform

Example:

mia-3dnonrigidreg -i test.v -r ref.v -o reg.v -l 2 -f spline:rate=3  image:cost=ssd divcurl:weight=10

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dlandmarks-transform	Home	mia-3dnonrigidreg-alt

│ │ │ + ...]

Description:

This program implements the registration of two gray scale 3D images.

Options:

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

IO

-i, --in-image=(input, required); io: test image. For supported file types see Plugin type: 3dimage/io
-r, --ref-image=(input, required); io: reference image. For supported file types see Plugin type: 3dimage/io
-o, --out-image=(output, required); io: registered output image. For supported file types see Plugin type: 3dimage/io
-t, --transformation=(output); io: output transformation. For supported file types see Plugin type: 3dtransform/io

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Registration

-l, --levels=3; ulong: multi-resolution levels
-O, --optimizer=gsl:opt=gd,step=0.1; factory: Optimizer used for minimization. For supported plug-ins see Plugin type: minimizer/singlecost
-f, --transForm=spline:rate=10; factory: transformation type. For supported plug-ins see Plugin type: 3dimage/transform

Example:

mia-3dnonrigidreg -i test.v -r ref.v -o reg.v -l 2 -f spline:rate=3  image:cost=ssd divcurl:weight=10

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dlandmarks-transform	Home	mia-3dnonrigidreg-alt

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dnonrigidregalt.html │ │ │ @@ -1,7 +1,7 @@ │ │ │ mia-3dnonrigidreg-alt

mia-3dnonrigidreg-alt
Prev	Registration, Comparison, and Transformation of 3D images	Next

mia-3dnonrigidreg-alt

Sysnopis:

mia-3dnonrigidreg-alt {-o io} [ │ │ │ options │ │ │ ...] [ │ │ │ │ │ │ Plugin type: 3dimage/fullcost │ │ │ │ │ │ - ...]

Description:

This program runs a non-rigid registration based on the given cost criteria and a given transformation model. Other than mia-3dnonrigidreg it doesn't support specific command line parameters to provide the images. Instead the images are specified dirctly when defining the cost function. Hence, image registrations can be executed that optimize the aligmnet of more than one image pair at the same time. Note, however, that all input images must be of the same dimension (in pixels)

Options:

-o, --out-transform=(required, output); io: output transformation. For supported file types see Plugin type: 3dtransform/io
-l, --levels=3; ulong: multi-resolution levels
-O, --optimizer=gsl:opt=gd,step=0.1; factory: Optimizer used for minimization. For supported plug-ins see Plugin type: minimizer/singlecost
-f, --transForm=spline:rate=10; factory: transformation type. For supported plug-ins see Plugin type: 3dimage/transform

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

mia-3dnonrigidreg-alt -o reg.vf -l 2 -f spline:rate=3 image:cost=ssd,src=test.v,ref=ref.v divcurl:weight=10

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dnonrigidreg	Home	mia-3drigidreg

│ │ │ + ...]

Description:

Options:

-o, --out-transform=(output, required); io: output transformation. For supported file types see Plugin type: 3dtransform/io
-l, --levels=3; ulong: multi-resolution levels
-O, --optimizer=gsl:opt=gd,step=0.1; factory: Optimizer used for minimization. For supported plug-ins see Plugin type: minimizer/singlecost
-f, --transForm=spline:rate=10; factory: transformation type. For supported plug-ins see Plugin type: 3dimage/transform

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

mia-3dnonrigidreg-alt -o reg.vf -l 2 -f spline:rate=3 image:cost=ssd,src=test.v,ref=ref.v divcurl:weight=10

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dnonrigidreg	Home	mia-3drigidreg

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dprealignnonrigid.html │ │ │ @@ -1,6 +1,6 @@ │ │ │ mia-3dprealign-nonrigid

mia-3dprealign-nonrigid
Prev	Registration of series of 3D images	Next

mia-3dprealign-nonrigid

Sysnopis:

mia-3dprealign-nonrigid {-i io} {-o io} [ │ │ │ options │ │ │ ...]

Description:

This program runs the non-rigid registration of an image series by first registering an already aligned subset of the images to one reference, and then by registering the remaining images by using synthetic references. This is a 3D version of

G. Wollny, M-J Ledesma-Cabryo, P.Kellman, and A.Santos, "Exploiting Quasiperiodicity in Motion Correction of Free-Breathing," IEEE Transactions on Medical Imaging, 29(8), 2010.

Options:

│ │ │ -File-IO

-i, --in-file=(required, input); io: input images following the naming pattern nameXXXX.ext. For supported file types see Plugin type: 3dimage/io
-o, --out-file=(required, output); io: file name base for registered files given as C-format string. For supported file types see Plugin type: 3dimage/io
--save-references: Save synthetic references to files refXXXX.v

│ │ │ +File-IO

-i, --in-file=(input, required); io: input images following the naming pattern nameXXXX.ext. For supported file types see Plugin type: 3dimage/io
-o, --out-file=(output, required); io: file name base for registered files given as C-format string. For supported file types see Plugin type: 3dimage/io
--save-references: Save synthetic references to files refXXXX.v

│ │ │ Preconditions & Preprocessing

-k, --skip=0; ulong: Skip images at the begin of the series
--preskip=20; ulong: Skip images at the beginning+skip of the series when searching for high contrats image
--postskip=2; ulong: Skip images at the end of the series when searching for high contrats image
--max-candidates=20; ulong: maximum number of candidates for global reference image
-S, --cost-series=image:cost=[ngf:eval=ds]; factory: Const function to use for the analysis of the series. For supported plug-ins see Plugin type: 3dimage/fullcost
--ref-idx=STRING: save reference index number to this file
-R, --global-reference=-1; int: save reference index number to this file
-D, --max-subset-delta=0; ulong: Maximum delta between two elements of the prealigned subset

│ │ │ Registration

-O, --optimizer=gsl:opt=gd,step=0.01; factory: Optimizer used for minimization. For supported plug-ins see Plugin type: minimizer/singlecost
-l, --mr-levels=3; ulong: multi-resolution levels
-f, --transForm=spline; factory: transformation type. For supported plug-ins see Plugin type: 3dimage/transform
-1, --cost-subset=image:cost=[ngf:eval=ds]; factory: Cost function for registration during the subset registration. For supported plug-ins see Plugin type: 3dimage/fullcost
-2, --cost-final=image:cost=ssd; factory: Cost function for registration during the final registration. For supported plug-ins see Plugin type: 3dimage/fullcost

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Register the image series given by images imageXXXX.v by optimizing a spline based transformation with a coefficient rate of 16 pixel, skipping two images at the beginning and using normalized gradient fields as initial cost measure and SSD as final measure. Penalize the transformation by using divcurl with aweight of 2.0. As optimizer an nlopt based newton method is used.

mia-3dprealign-nonrigid mia-3dprealign-nonrigid  -i imageXXXX.v -o registered -t vista -k 2-F spline:rate=16,penalty=[divcurl:weight=2] -1 image:cost=[ngf:eval=ds] -2 image:cost=ssd -O nlopt:opt=ld-var1,xtola=0.001,ftolr=0.001,maxiter=300

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dmotioncompica-nonrigid	Home	mia-3dserial-nonrigid

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dproposeboundingbox.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-3dpropose-boundingbox

mia-3dpropose-boundingbox
Prev	Analysis, filtering, combining, and segmentation of 3D images	Next

mia-3dpropose-boundingbox

Sysnopis:

mia-3dpropose-boundingbox {-i io} [ │ │ │ options │ │ │ - ...]

Description:

This program evaluates a box that contains all the pixels of a given mask image. If the input image is not a binary image, a pre-filter must be applied that converts the imput image into a mask.

Options:

File-IO

-i, --in-file=(required, input); io: input image(s) to be filtered. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Parameters

-f, --filter=: Filter to be applied to the image before the bounding box is evaluated. Must return a bit-valued image.. For supported plug-ins see Plugin type: 3dimage/filter
-p, --padding=0; uint in [0, inf): Padding of boundaries.

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate a bounding box with boundary padding of 5 of a mask resulting from a binarization with a minimum value 10.10 and a boundary padding of 5 from image image.v .

mia-3dpropose-boundingbox -i image.v -f binarize:min=10 -p 5

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dmaskseeded	Home	mia-3dsegment-ahmed

│ │ │ + ...]

Description:

This program evaluates a box that contains all the pixels of a given mask image. If the input image is not a binary image, a pre-filter must be applied that converts the imput image into a mask.

Options:

File-IO

-i, --in-file=(input, required); io: input image(s) to be filtered. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Parameters

-f, --filter=: Filter to be applied to the image before the bounding box is evaluated. Must return a bit-valued image.. For supported plug-ins see Plugin type: 3dimage/filter
-p, --padding=0; uint in [0, inf): Padding of boundaries.

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate a bounding box with boundary padding of 5 of a mask resulting from a binarization with a minimum value 10.10 and a boundary padding of 5 from image image.v .

mia-3dpropose-boundingbox -i image.v -f binarize:min=10 -p 5

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dmaskseeded	Home	mia-3dsegment-ahmed

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3drigidreg.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-3drigidreg

mia-3drigidreg
Prev	Registration, Comparison, and Transformation of 3D images	Next

mia-3drigidreg

Sysnopis:

mia-3drigidreg {-i io} {-r io} {-o io} [ │ │ │ options │ │ │ - ...]

Description:

This program implements the registration of two gray scale 3D images. The transformation is not penalized, therefore, one should only use translation, rigid, or affine transformations as target and run mia-3dnonrigidreg of nonrigid registration is to be achieved.

Options:

File I/O

-i, --in-image=(required, input); io: test image. For supported file types see Plugin type: 3dimage/io
-r, --ref-image=(required, input); io: reference image. For supported file types see Plugin type: 3dimage/io
-o, --out-image=(required, output); io: registered output image. For supported file types see Plugin type: 3dimage/io
-t, --transformation=(output); io: transformation output file name. For supported file types see Plugin type: 3dtransform/io
-c, --cost=ssd; factory: cost function. For supported plug-ins see Plugin type: 3dimage/cost
-l, --levels=3; ulong: multigrid levels
-O, --optimizer=gsl:opt=simplex,step=1.0; factory: Optimizer used for minimization. For supported plug-ins see Plugin type: minimizer/singlecost
-f, --transForm=rigid; factory: transformation type. For supported plug-ins see Plugin type: 3dimage/transform

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Register image test.v to image ref.v affine and write the registered image to reg.v. Use two multiresolution levels and ssd as cost function.

mia-3drigidreg -i test.v -r ref.v -o reg.v -l 2 -f affine -c ssd

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dnonrigidreg-alt	Home	mia-3dtransform

│ │ │ + ...]

Description:

Options:

File I/O

-i, --in-image=(input, required); io: test image. For supported file types see Plugin type: 3dimage/io
-r, --ref-image=(input, required); io: reference image. For supported file types see Plugin type: 3dimage/io
-o, --out-image=(output, required); io: registered output image. For supported file types see Plugin type: 3dimage/io
-t, --transformation=(output); io: transformation output file name. For supported file types see Plugin type: 3dtransform/io
-c, --cost=ssd; factory: cost function. For supported plug-ins see Plugin type: 3dimage/cost
-l, --levels=3; ulong: multigrid levels
-O, --optimizer=gsl:opt=simplex,step=1.0; factory: Optimizer used for minimization. For supported plug-ins see Plugin type: minimizer/singlecost
-f, --transForm=rigid; factory: transformation type. For supported plug-ins see Plugin type: 3dimage/transform

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Register image test.v to image ref.v affine and write the registered image to reg.v. Use two multiresolution levels and ssd as cost function.

mia-3drigidreg -i test.v -r ref.v -o reg.v -l 2 -f affine -c ssd

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dnonrigidreg-alt	Home	mia-3dtransform

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dsegmentahmed.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-3dsegment-ahmed

mia-3dsegment-ahmed
Prev	Analysis, filtering, combining, and segmentation of 3D images	Next

mia-3dsegment-ahmed

Sysnopis:

mia-3dsegment-ahmed {-i io} {-c io} [ │ │ │ options │ │ │ - ...]

Description:

This program implements a variation of the paper:

Mohamed N. Ahmed et. al, "A Modified Fuzzy C-Means Algorithm for Bias Field estimation and Segmentation of MRI Data", IEEE Trans. on Medical Imaging, Vol. 21, No. 3, March 2002,

changes are: p=2, and exp

Options:

File-IO

-i, --in-file=(required, input); io: image to be segmented. For supported file types see Plugin type: 3dimage/io
-c, --class-file=(required, output); io: class probability images, the image type must support multiple images and floating point values. For supported file types see Plugin type: 3dimage/io
-b, --out-file=(output); io: Bias corrected image will be of the same type like the input image. If this parameter is not given, then the bias correction will not be applied.. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Parameters

-n, --no-of-classes=3; int: number of classes
-C, --class-centres=: initial class centers, this parameter overrides 'no-of-clases'.
-s, --spread=64; float: spread parameter describing the strength of mattar distinction

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run a 5-class segmentation over input image input.v and store the class probability images in cls.v.

mia-3dsegment-ahmed -i input.v -a 5 -o cls.v

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dpropose-boundingbox	Home	mia-3dsegment-local-cmeans

│ │ │ + ...]

Description:

This program implements a variation of the paper:

Mohamed N. Ahmed et. al, "A Modified Fuzzy C-Means Algorithm for Bias Field estimation and Segmentation of MRI Data", IEEE Trans. on Medical Imaging, Vol. 21, No. 3, March 2002,

changes are: p=2, and exp

Options:

File-IO

-i, --in-file=(input, required); io: image to be segmented. For supported file types see Plugin type: 3dimage/io
-c, --class-file=(output, required); io: class probability images, the image type must support multiple images and floating point values. For supported file types see Plugin type: 3dimage/io
-b, --out-file=(output); io: Bias corrected image will be of the same type like the input image. If this parameter is not given, then the bias correction will not be applied.. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Parameters

-n, --no-of-classes=3; int: number of classes
-C, --class-centres=: initial class centers, this parameter overrides 'no-of-clases'.
-s, --spread=64; float: spread parameter describing the strength of mattar distinction

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run a 5-class segmentation over input image input.v and store the class probability images in cls.v.

mia-3dsegment-ahmed -i input.v -a 5 -o cls.v

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dpropose-boundingbox	Home	mia-3dsegment-local-cmeans

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dsegmentlocalcmeans.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-3dsegment-local-cmeans

mia-3dsegment-local-cmeans
Prev	Analysis, filtering, combining, and segmentation of 3D images	Next

mia-3dsegment-local-cmeans

Sysnopis:

mia-3dsegment-local-cmeans {-i io} [ │ │ │ options │ │ │ - ...]

Description:

This program runs the segmentation of a 3D image by applying a localized c-means approach that helps to overcome intensity inhomogeneities in the image. The approach evaluates a global c-means clustering, and then separates the image into overlapping regions where more c-means iterations are run only including the locally present classes, i.e. the classes that relatively contain more pixels than a given threshold. This program implements algorithm described in:

Dunmore CJ, Wollny G, Skinner MM. (2018) MIA-Clustering: a novel method for segmentation of paleontological material. PeerJ 6:e4374.

Options:

File-IO

-i, --in-file=(required, input); io: image to be segmented. For supported file types see Plugin type: 3dimage/io
-o, --out-file=(output); io: class label image based on merging local labels. For supported file types see Plugin type: 3dimage/io
-G, --out-global-crisp=(output); io: class label image based on global segmentation. For supported file types see Plugin type: 3dimage/io
-C, --class-prob=(output); io: class probability image file, filetype must support floating point multi-frame images. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Parameters

-g, --grid-spacing=15; int in [3, inf): Spacing of the grid used to modulate the intensity inhomogeneities
-c, --cmeans=kmeans:nc=3; factory: c-means initializer. For supported plug-ins see Plugin type: 1d/cmeans
-e, --c-means-epsilon=0.0001; float in (0, inf): c-means breaking condition for update tolerance
-t, --relative-cluster-threshold=0.02; double in [0, 1): threshhold to ignore classes when initializing the local cmeans from the global one.
-B, --ignore-background: Don't take background probablities into account when desiding whether classes are to be ignored
-L, --label-threshold=0; float in [0, 1]: for values <= 0.5: create segmentation based on highest class probability, labels start at 0. For values >0.5: create labels only for voxels with a class probability higher than the given value, labels start at 1 and voxels without an according class probability are set to 0; this output is suitable for the seeded watershed filter.

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run the segmentation on image test.png using three classes, local regions of 40 pixels (grid width 20 pixels), and a class ignore threshold of 0.01.

mia-3dsegment-local-cmeans -i test.png -o label.png -n 3 -g 20 -t 0.01

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dsegment-ahmed	Home	Registration, Comparison, and Transformation of 3D images

│ │ │ + ...]

Description:

Dunmore CJ, Wollny G, Skinner MM. (2018) MIA-Clustering: a novel method for segmentation of paleontological material. PeerJ 6:e4374.

Options:

File-IO

-i, --in-file=(input, required); io: image to be segmented. For supported file types see Plugin type: 3dimage/io
-o, --out-file=(output); io: class label image based on merging local labels. For supported file types see Plugin type: 3dimage/io
-G, --out-global-crisp=(output); io: class label image based on global segmentation. For supported file types see Plugin type: 3dimage/io
-C, --class-prob=(output); io: class probability image file, filetype must support floating point multi-frame images. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Parameters

-g, --grid-spacing=15; int in [3, inf): Spacing of the grid used to modulate the intensity inhomogeneities
-c, --cmeans=kmeans:nc=3; factory: c-means initializer. For supported plug-ins see Plugin type: 1d/cmeans
-e, --c-means-epsilon=0.0001; float in (0, inf): c-means breaking condition for update tolerance
-t, --relative-cluster-threshold=0.02; double in [0, 1): threshhold to ignore classes when initializing the local cmeans from the global one.
-B, --ignore-background: Don't take background probablities into account when desiding whether classes are to be ignored
-L, --label-threshold=0; float in [0, 1]: for values <= 0.5: create segmentation based on highest class probability, labels start at 0. For values >0.5: create labels only for voxels with a class probability higher than the given value, labels start at 1 and voxels without an according class probability are set to 0; this output is suitable for the seeded watershed filter.

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run the segmentation on image test.png using three classes, local regions of 40 pixels (grid width 20 pixels), and a class ignore threshold of 0.01.

mia-3dsegment-local-cmeans -i test.png -o label.png -n 3 -g 20 -t 0.01

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dsegment-ahmed	Home	Registration, Comparison, and Transformation of 3D images

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dserialnonrigid.html │ │ │ @@ -1,9 +1,9 @@ │ │ │ mia-3dserial-nonrigid

mia-3dserial-nonrigid
Prev	Registration of series of 3D images	Next

mia-3dserial-nonrigid

Sysnopis:

mia-3dserial-nonrigid {-i string} [ │ │ │ options │ │ │ ...] [ │ │ │ │ │ │ Plugin type: 3dimage/fullcost │ │ │ │ │ │ ...]

Description:

This program runs the image registration of a consecutively numbered image series. The registration is run in a serial manner, this is, only images in temporal succession (i.e. consecutive numbers) are registered, and the obtained transformations are applied accumulated to reach full registration.

Options:

│ │ │ -File-IO

-i, --in-file=(required, input); string: input perfusion data set
-o, --out-file=(output); string: file name for registered fiels

│ │ │ +File-IO

-i, --in-file=(input, required); string: input perfusion data set
-o, --out-file=(output); string: file name for registered fiels

│ │ │ Registration

-O, --optimizer=gsl:opt=gd,step=0.1; factory: Optimizer used for minimization. For supported plug-ins see Plugin type: minimizer/singlecost
-l, --mg-levels=3; ulong: multi-resolution levels
-f, --transForm=spline; factory: transformation type. For supported plug-ins see Plugin type: 3dimage/transform
-r, --ref=-1; int: reference frame (-1 == use image in the middle)

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run a serial registration of images inputXXXX.v (X digit) to reference image 20 and store the result in regXXXX.v. Optimize the sum of squared differences and spline transformations with coefficient rate 10.

mia-3dserial-nonrigid -i input0000.v -o 'reg%04d.v' -f spline:rate=10 -r 20 ssd

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dprealign-nonrigid	Home	Tools for the Analysis of 3D image series

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dseriestrackintensity.html │ │ │ @@ -1,4 +1,4 @@ │ │ │ mia-3dseries-track-intensity

mia-3dseries-track-intensity
Prev	Tools for the Analysis of 3D image series	Next

mia-3dseries-track-intensity

Sysnopis:

mia-3dseries-track-intensity {-i io} {-o string} [ │ │ │ options │ │ │ ...]

Description:

This program tracks the intensity of a pixel at the given coordinates.

Options:

│ │ │ -File-IO

-i, --in-file=(required, input); io: input perfusion data set. For supported file types see Plugin type: 3dimage/io
-o, --out-file=(required, output); string: file name for output intensity slopes

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the intensity-time curves at points <12,13,14> and <222,113,214>

mia-3dseries-track-intensity -i images0000.v -o curves.txt '<12,13,14>' '<222,113,214>'

Author(s):

Gert Wollny

Prev	Up	Next
mia-3deval-transformquantity	Home	mia-3dtrackpixelmovement

│ │ │ +File-IO

-i, --in-file=(input, required); io: input perfusion data set. For supported file types see Plugin type: 3dimage/io
-o, --out-file=(output, required); string: file name for output intensity slopes

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the intensity-time curves at points <12,13,14> and <222,113,214>

mia-3dseries-track-intensity -i images0000.v -o curves.txt '<12,13,14>' '<222,113,214>'

Author(s):

Gert Wollny

Prev	Up	Next
mia-3deval-transformquantity	Home	mia-3dtrackpixelmovement

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dtrackpixelmovement.html │ │ │ @@ -1,8 +1,8 @@ │ │ │ mia-3dtrackpixelmovement

mia-3dtrackpixelmovement
Prev	Tools for the Analysis of 3D image series	Next

mia-3dtrackpixelmovement

Sysnopis:

mia-3dtrackpixelmovement {-i string} {-o string} {-t io} [ │ │ │ options │ │ │ ...]

Description:

Options:

│ │ │ -File-IO

-i, --in-file=(required, input); string: input point set
-o, --out-file=(required, output); string: output point set
-t, --transformation=(required, input); io: transformation describing the monitored change. For supported file types see Plugin type: 3dtransform/io

│ │ │ +File-IO

-i, --in-file=(input, required); string: input point set
-o, --out-file=(output, required); string: output point set
-t, --transformation=(input, required); io: transformation describing the monitored change. For supported file types see Plugin type: 3dtransform/io

│ │ │ Parameters

-T, --time-step=1; float: time step to use for the position update

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

This program evaluated the changed position of pixels given in input.csv, by using a time step of 2.0 time units and the transformation change.v3df, and writes the updated positions to updated.csv.

mia-3dtrackpixelmovement -i input.csv -o output.cvs --time-step 2.0 --transformation change.v3df

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dseries-track-intensity	Home	Miscellaneous programs

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dtransform.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-3dtransform

mia-3dtransform
Prev	Registration, Comparison, and Transformation of 3D images	Next

mia-3dtransform

Sysnopis:

mia-3dtransform {-i io} {-o io} {-t io} [ │ │ │ options │ │ │ - ...]

Description:

Transform a 3D image by applying a given 3D transformation.

Options:

-i, --in-file=(required, input); io: input image. For supported file types see Plugin type: 3dimage/io
-o, --out-file=(required, output); io: transformed image. For supported file types see Plugin type: 3dimage/io
-t, --transformation=(required, input); io: transformation file. For supported file types see Plugin type: 3dtransform/io
-p, --interpolator=STRING: override the interpolator provided by the transformation
-b, --boundary=mirror; stringSTRING: override the boundary conditions provided by the transformation. This is only used if the interpolator is also overridden.

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Transform an image input.v by the transfromation stored in trans.v by using nearest neighbour interpolation ans store the result in output.v

mia-3dtransform -i input.v -t trans.v  -o output.v  -p bspline:d=0

Author(s):

Gert Wollny

Prev	Up	Next
mia-3drigidreg	Home	mia-3dtransform2vf

│ │ │ + ...]

Description:

Transform a 3D image by applying a given 3D transformation.

Options:

-i, --in-file=(input, required); io: input image. For supported file types see Plugin type: 3dimage/io
-o, --out-file=(output, required); io: transformed image. For supported file types see Plugin type: 3dimage/io
-t, --transformation=(input, required); io: transformation file. For supported file types see Plugin type: 3dtransform/io
-p, --interpolator=STRING: override the interpolator provided by the transformation
-b, --boundary=mirror; stringSTRING: override the boundary conditions provided by the transformation. This is only used if the interpolator is also overridden.

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Transform an image input.v by the transfromation stored in trans.v by using nearest neighbour interpolation ans store the result in output.v

mia-3dtransform -i input.v -t trans.v  -o output.v  -p bspline:d=0

Author(s):

Gert Wollny

Prev	Up	Next
mia-3drigidreg	Home	mia-3dtransform2vf

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dtransform2vf.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-3dtransform2vf

mia-3dtransform2vf
Prev	Registration, Comparison, and Transformation of 3D images	Next

mia-3dtransform2vf

Sysnopis:

mia-3dtransform2vf {-i io} {-o io} [ │ │ │ options │ │ │ - ...]

Description:

Create a 3D vector field from a given transformation. The output vector field will have the dimesions as given in the transformation description.

Options:

-i, --in-file=(required, input); io: input transformation . For supported file types see Plugin type: 3dtransform/io
-o, --out-file=(required, output); io: output vector field . For supported file types see Plugin type: 3dvf/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Transform the input transformation trans.v3df to a vector field field.vtk.

mia-3dtransform2vf -i trans.v3df   -o field.vtk

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dtransform	Home	mia-3dvf2transform

│ │ │ + ...]

Description:

Create a 3D vector field from a given transformation. The output vector field will have the dimesions as given in the transformation description.

Options:

-i, --in-file=(input, required); io: input transformation . For supported file types see Plugin type: 3dtransform/io
-o, --out-file=(output, required); io: output vector field . For supported file types see Plugin type: 3dvf/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Transform the input transformation trans.v3df to a vector field field.vtk.

mia-3dtransform2vf -i trans.v3df   -o field.vtk

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dtransform	Home	mia-3dvf2transform

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dvectorfieldcreate.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-3dvectorfieldcreate

mia-3dvectorfieldcreate
Prev	Miscellaneous programs	Next

mia-3dvectorfieldcreate

Sysnopis:

mia-3dvectorfieldcreate {-o io} [ │ │ │ options │ │ │ - ...]

Description:

This program is used to create a file containing a 3D vector field.

Options:

-o, --out-file=(required, output); io: output file for the vector field. For supported file types see Plugin type: 3dvf/io
-s, --size=[64,64,64]; 3dbounds: size of the vector field
-y, --ftype=0; short: vector field type
-f, --fun=1; float: just some parameter to vary the field ;-)

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Create a field of type 2 with fun 3.0 and size 128x128x128.

mia-3dvectorfieldcreate -o field.v -s '<128,128,128>' -t 2 -f 3.0

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dimageaddattributes	Home	mia-cmeans

│ │ │ + ...]

Description:

This program is used to create a file containing a 3D vector field.

Options:

-o, --out-file=(output, required); io: output file for the vector field. For supported file types see Plugin type: 3dvf/io
-s, --size=[64,64,64]; 3dbounds: size of the vector field
-y, --ftype=0; short: vector field type
-f, --fun=1; float: just some parameter to vary the field ;-)

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Create a field of type 2 with fun 3.0 and size 128x128x128.

mia-3dvectorfieldcreate -o field.v -s '<128,128,128>' -t 2 -f 3.0

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dimageaddattributes	Home	mia-cmeans

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dvf2transform.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-3dvf2transform

mia-3dvf2transform
Prev	Registration, Comparison, and Transformation of 3D images	Next

mia-3dvf2transform

Sysnopis:

mia-3dvf2transform {-i io} {-o io} [ │ │ │ options │ │ │ - ...]

Description:

Creates a 3D transformation from a vector field. The input vector field is simply encapsulated into the transformation file format. The boundary conditions and the image interpolator kernel can be set at the command line.

Options:

-i, --in-file=(required, input); io: input transformation . For supported file types see Plugin type: 3dvf/io
-o, --out-file=(required, output); io: output vector field . For supported file types see Plugin type: 3dtransform/io
-k, --imgkernel=bspline:d=3; factory: image interpolator kernel which is used when the transformation is applied to an image. For supported plug-ins see Plugin type: 1d/splinekernel
-b, --imgboundary=mirror; factory: Boundary condition applied when the transformation is used to transform an image. For supported plug-ins see Plugin type: 1d/splinebc

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Transform the input vector field field.vtk to the transformation trans.v3df and specify zero boundary conditions and b-splines of degree 2 for image interpolation.

mia-3dvf2transform -i field.vtk -o trans.v3df --imgkernel bspline:d=2 --imgboundary zero

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dtransform2vf	Home	mia-3dvfcompare

│ │ │ + ...]

Description:

Options:

-i, --in-file=(input, required); io: input transformation . For supported file types see Plugin type: 3dvf/io
-o, --out-file=(output, required); io: output vector field . For supported file types see Plugin type: 3dtransform/io
-k, --imgkernel=bspline:d=3; factory: image interpolator kernel which is used when the transformation is applied to an image. For supported plug-ins see Plugin type: 1d/splinekernel
-b, --imgboundary=mirror; factory: Boundary condition applied when the transformation is used to transform an image. For supported plug-ins see Plugin type: 1d/splinebc

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Transform the input vector field field.vtk to the transformation trans.v3df and specify zero boundary conditions and b-splines of degree 2 for image interpolation.

mia-3dvf2transform -i field.vtk -o trans.v3df --imgkernel bspline:d=2 --imgboundary zero

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dtransform2vf	Home	mia-3dvfcompare

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dvfcompare.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-3dvfcompare

mia-3dvfcompare
Prev	Registration, Comparison, and Transformation of 3D images	Next

mia-3dvfcompare

Sysnopis:

mia-3dvfcompare {-1 io} {-2 io} [ │ │ │ options │ │ │ - ...]

Description:

Compare two vector fields and print the out the difference norm per pixel to cout it it is larger than delta.

Options:

-1, --in-file-1=(required, input); io: input vector field 1. For supported file types see Plugin type: 3dvf/io
-2, --in-file-2=(required, input); io: input vector field 2. For supported file types see Plugin type: 3dvf/io
-d, --delta=0; float: Maximum difference between vector to be ignored

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Compare vector fields vf1.v and vf2.v and print out all differences above 0.01.

mia-3dvfcompare -1 vf1.v -2 vf2.v -d 0.01

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dvf2transform	Home	Registration of series of 3D images

│ │ │ + ...]

Description:

Compare two vector fields and print the out the difference norm per pixel to cout it it is larger than delta.

Options:

-1, --in-file-1=(input, required); io: input vector field 1. For supported file types see Plugin type: 3dvf/io
-2, --in-file-2=(input, required); io: input vector field 2. For supported file types see Plugin type: 3dvf/io
-d, --delta=0; float: Maximum difference between vector to be ignored

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Compare vector fields vf1.v and vf2.v and print out all differences above 0.01.

mia-3dvfcompare -1 vf1.v -2 vf2.v -d 0.01

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dvf2transform	Home	Registration of series of 3D images

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmiacmeans.html │ │ │ @@ -1,4 +1,4 @@ │ │ │ mia-cmeans

mia-cmeans
Prev	Miscellaneous programs	Next

mia-cmeans

Sysnopis:

mia-cmeans {-i string} {-o string} [ │ │ │ options │ │ │ - ...]

Description:

This Program reads a histogram from stdin and evaluates a cmeans classification of the intensity values into the given number of classes.

Options:

-i, --in-file=(required, input); string: input file name containing the histogram
-o, --out-file=(required, output); string: output file name to store probabilities
-n, --nclasses=3; int: number of classes to partition into
-m, --max-iter=100; int: maximum number of iterations
-e, --even-start: start with centers evenly distributed over the histogram
-c, --class-centers=: initial class centers
-a, --auto: atomatic adaption of variance (experimental)
-t, --cut-histo: cut empty histogram at the end
-k, --variance=1; double: variance parameter
--self-test: run self test

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

│ │ │ + ...]

Description:

This Program reads a histogram from stdin and evaluates a cmeans classification of the intensity values into the given number of classes.

Options:

-i, --in-file=(input, required); string: input file name containing the histogram
-o, --out-file=(output, required); string: output file name to store probabilities
-n, --nclasses=3; int: number of classes to partition into
-m, --max-iter=100; int: maximum number of iterations
-e, --even-start: start with centers evenly distributed over the histogram
-c, --class-centers=: initial class centers
-a, --auto: atomatic adaption of variance (experimental)
-t, --cut-histo: cut empty histogram at the end
-k, --variance=1; double: variance parameter
--self-test: run self test

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

│ │ │

mia-cmeans

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dvectorfieldcreate	Home	mia-filenumberpattern

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmiafilenumberpattern.html │ │ │ @@ -1,4 +1,4 @@ │ │ │ mia-filenumberpattern

mia-filenumberpattern
Prev	Miscellaneous programs	Next

mia-filenumberpattern

Sysnopis:

mia-filenumberpattern {-i string} [ │ │ │ options │ │ │ - ...]

Description:

This program is used to extract a extract the number pattern for file012312.ext type file names.

Options:

-i, --in-file=(required, input); string: input image example name

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

│ │ │ + ...]

Description:

This program is used to extract a extract the number pattern for file012312.ext type file names.

Options:

-i, --in-file=(input, required); string: input image example name

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

│ │ │

mia-filenumberpattern

Author(s):

Gert Wollny

Prev	Up	Next
mia-cmeans	Home	mia-labelsort

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmialabelsort.html │ │ │ @@ -1,4 +1,4 @@ │ │ │ mia-labelsort

mia-labelsort
Prev	Miscellaneous programs	Next

mia-labelsort

Sysnopis:

mia-labelsort {-i string} {-o string} [ │ │ │ options │ │ │ - ...]

Description:

This program is used create a mapping based on a histogram that puts the intensities with high values at the beginning of the histogram. The main use case will be to sort labels of connected components in out-of-core image processing.

Options:

-i, --in-file=(required, input); string: input file name containing the histogram
-o, --out-file=(required, output); string: output file name to store probabilities

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

│ │ │ + ...]

Description:

Options:

-i, --in-file=(input, required); string: input file name containing the histogram
-o, --out-file=(output, required); string: output file name to store probabilities

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

│ │ │

mia-labelsort

Author(s):

Gert Wollny

Prev	Up	Next
mia-filenumberpattern	Home	mia-myowavelettest

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmiameshdeformablemodel.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-mesh-deformable-model

mia-mesh-deformable-model
Prev	Creation, analysis, and filtering of triangular 3D meshes	Next

mia-mesh-deformable-model

Sysnopis:

mia-mesh-deformable-model {-i io} {-o io} {-r io} [ │ │ │ options │ │ │ - ...]

Description:

This program runs a deformable model to adapt a mesh to an iso-value within a given image. <FIXME: Reference>

Options:

File I/O

-i, --in-file=(required, input); io: input mesh to be adapted. For supported file types see Plugin type: mesh/io
-o, --out-file=(required, output); io: output mesh that has been deformed. For supported file types see Plugin type: mesh/io
-r, --ref-file=(required, input); io: reference image. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Model parameters

--smoothing-weight=0.04; float in [0, inf): Weight of the inner force used to smooth the mesh
--gradient-weight=0.04; float: Weight of the gradient force drive the mesh deformation. Use a negative value to invert the search direction.
--intensity-weight=0.02; float in [0, inf): Weight of the force resulting from the intensity difference at the vertex position versus the reference intensity 'iso'.
--intensity-scaling=1; float in (0, inf): Scaling of the raw intensity difference.
-s, --iso=64; float: Intensity value the mesh verices should adapt to.

Preprocessing

--image-smoothing=gauss:w=2; factory: Prefilter to smooth the reference image.. For supported plug-ins see Plugin type: 3dimage/filter

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).
-m, --maxiter=200; uint in (0, inf): Maximum number of iterations.
-e, --epsilon=0.001; float in (0, inf): Stop iteration when the maximum shift of the vertices falls below this value
--reorient: Reorientate the mesh triangles

Example:

Run the deforemable model on input.vmesh with 200 iterations adapting to a value of 128 in the image ref.v and save the result to deformed.vmesh

mia-mesh-deformable-model -i input.vmesh -o deformed.vmesh --iso 128 --maxiter 200

Author(s):

Gert Wollny

Prev	Up	Next
mia-3disosurface-from-volume	Home	mia-mesh-to-maskimage

│ │ │ + ...]

Description:

This program runs a deformable model to adapt a mesh to an iso-value within a given image. <FIXME: Reference>

Options:

File I/O

-i, --in-file=(input, required); io: input mesh to be adapted. For supported file types see Plugin type: mesh/io
-o, --out-file=(output, required); io: output mesh that has been deformed. For supported file types see Plugin type: mesh/io
-r, --ref-file=(input, required); io: reference image. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Model parameters

--smoothing-weight=0.04; float in [0, inf): Weight of the inner force used to smooth the mesh
--gradient-weight=0.04; float: Weight of the gradient force drive the mesh deformation. Use a negative value to invert the search direction.
--intensity-weight=0.02; float in [0, inf): Weight of the force resulting from the intensity difference at the vertex position versus the reference intensity 'iso'.
--intensity-scaling=1; float in (0, inf): Scaling of the raw intensity difference.
-s, --iso=64; float: Intensity value the mesh verices should adapt to.

Preprocessing

--image-smoothing=gauss:w=2; factory: Prefilter to smooth the reference image.. For supported plug-ins see Plugin type: 3dimage/filter

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).
-m, --maxiter=200; uint in (0, inf): Maximum number of iterations.
-e, --epsilon=0.001; float in (0, inf): Stop iteration when the maximum shift of the vertices falls below this value
--reorient: Reorientate the mesh triangles

Example:

Run the deforemable model on input.vmesh with 200 iterations adapting to a value of 128 in the image ref.v and save the result to deformed.vmesh

mia-mesh-deformable-model -i input.vmesh -o deformed.vmesh --iso 128 --maxiter 200

Author(s):

Gert Wollny

Prev	Up	Next
mia-3disosurface-from-volume	Home	mia-mesh-to-maskimage

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmiameshdistancetostackmask.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-meshdistance-to-stackmask

mia-meshdistance-to-stackmask
Prev	Creation, analysis, and filtering of triangular 3D meshes	Next

mia-meshdistance-to-stackmask

Sysnopis:

mia-meshdistance-to-stackmask {-i io} {-r io} {-o io} [ │ │ │ options │ │ │ - ...]

Description:

This program takes a binary masks and a triangular mesh as input and evaluates the distance of the mesh vertices to the binary maskand stores the result in a new mesh.

Options:

-i, --in-mesh=(required, input); io: input mesh. For supported file types see Plugin type: mesh/io
-r, --ref-mask=(required, input); io: reference binary mask. For supported file types see Plugin type: 2dimage/io
-o, --out-mesh=(required, output); io: output mesh. For supported file types see Plugin type: mesh/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the distance of the mask given in the images maskXXXX.png to the mesh given in mesh.v and save the result to mesh-dist.v

mia-meshdistance-to-stackmask -i mesh.v -r maskXXXX.png -o mesh-dist.v

Author(s):

Gert Wollny

Prev	Up	Next
mia-mesh-to-maskimage	Home	mia-meshfilter

│ │ │ + ...]

Description:

This program takes a binary masks and a triangular mesh as input and evaluates the distance of the mesh vertices to the binary maskand stores the result in a new mesh.

Options:

-i, --in-mesh=(input, required); io: input mesh. For supported file types see Plugin type: mesh/io
-r, --ref-mask=(input, required); io: reference binary mask. For supported file types see Plugin type: 2dimage/io
-o, --out-mesh=(output, required); io: output mesh. For supported file types see Plugin type: mesh/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the distance of the mask given in the images maskXXXX.png to the mesh given in mesh.v and save the result to mesh-dist.v

mia-meshdistance-to-stackmask -i mesh.v -r maskXXXX.png -o mesh-dist.v

Author(s):

Gert Wollny

Prev	Up	Next
mia-mesh-to-maskimage	Home	mia-meshfilter

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmiameshfilter.html │ │ │ @@ -2,8 +2,8 @@ │ │ │ options │ │ │ ...] [ │ │ │ │ │ │ Plugin type: mesh/filter │ │ │ │ │ │ ...]

Description:

This program runs a series filters on a given input mesh. The filters are given as extra parameters on the command line and are run in the order in which they are given. To obtain a list of available filters you may run │ │ │ 'mia-plugin-help mesh/filter' │ │ │ -from the command line

Options:

-i, --in-file=(required, input); io: input mesh to be filtered. For supported file types see Plugin type: mesh/io
-o, --out-file=(required, output); io: output mesh that have been filtered. For supported file types see Plugin type: mesh/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run an isotropic scaling on input.vmesh to fit it into the box defined by the corners <0,0,0> - <128,128,128> and save the result to output.vmesh

mia-meshfilter -i input.vmesh -o output.vmesh scale:strategy=iso-fitbox,box-start=[<0,0,0>],box-end=[<128,128,128>]

Author(s):

Gert Wollny

Prev	Up	Next
mia-meshdistance-to-stackmask	Home	Help

│ │ │ +from the command line

Options:

-i, --in-file=(input, required); io: input mesh to be filtered. For supported file types see Plugin type: mesh/io
-o, --out-file=(output, required); io: output mesh that have been filtered. For supported file types see Plugin type: mesh/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run an isotropic scaling on input.vmesh to fit it into the box defined by the corners <0,0,0> - <128,128,128> and save the result to output.vmesh

mia-meshfilter -i input.vmesh -o output.vmesh scale:strategy=iso-fitbox,box-start=[<0,0,0>],box-end=[<128,128,128>]

Author(s):

Gert Wollny

Prev	Up	Next
mia-meshdistance-to-stackmask	Home	Help

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmiameshtomaskimage.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-mesh-to-maskimage

mia-mesh-to-maskimage
Prev	Creation, analysis, and filtering of triangular 3D meshes	Next

mia-mesh-to-maskimage

Sysnopis:

mia-mesh-to-maskimage {-i io} {-o io} [ │ │ │ options │ │ │ - ...]

Description:

This program converts a 3D mesh into a binary mask comprising the mesh surface. The output image size is either given on the command line or deducted from the mesh dimensions.

Options:

File I/O

-i, --in-file=(required, input); io: input mesh to be adapted. For supported file types see Plugin type: mesh/io
-o, --out-file=(required, output); io: output image containing the binary mask. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Properties

--origin=[0,0,0]; 3dfvector: coordinate of pixel at index 0,0,0
--spacing=[1,1,1]; 3dfvector: voxel spacing in the output image, all values must be positive.
--size=[0,0,0]; 3dbounds: size of the output image (0,0,0 = deduct)

Example:

The input mesh input.vmesh is converted into the binary mask mask.v. The image size is set to 50,50,50 and the size is obtained automatically to include the whole mesh

mia-mesh-to-maskimage -i input.vmesh -o mask.v --origin 0,0,0

Author(s):

Gert Wollny

Prev	Up	Next
mia-mesh-deformable-model	Home	mia-meshdistance-to-stackmask

│ │ │ + ...]

Description:

This program converts a 3D mesh into a binary mask comprising the mesh surface. The output image size is either given on the command line or deducted from the mesh dimensions.

Options:

File I/O

-i, --in-file=(input, required); io: input mesh to be adapted. For supported file types see Plugin type: mesh/io
-o, --out-file=(output, required); io: output image containing the binary mask. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Properties

--origin=[0,0,0]; 3dfvector: coordinate of pixel at index 0,0,0
--spacing=[1,1,1]; 3dfvector: voxel spacing in the output image, all values must be positive.
--size=[0,0,0]; 3dbounds: size of the output image (0,0,0 = deduct)

Example:

The input mesh input.vmesh is converted into the binary mask mask.v. The image size is set to 50,50,50 and the size is obtained automatically to include the whole mesh

mia-mesh-to-maskimage -i input.vmesh -o mask.v --origin 0,0,0

Author(s):

Gert Wollny

Prev	Up	Next
mia-mesh-deformable-model	Home	mia-meshdistance-to-stackmask

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmiamultihist.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-multihist

mia-multihist
Prev	Processing of series of 2D images in a 3D fashion (out-of-core)	Next

mia-multihist

Sysnopis:

mia-multihist {-i io} {-o string} [ │ │ │ options │ │ │ - ...]

Description:

This program evaluates the histogram over a series of 2D images

Options:

-i, --in-file=(required, input); io: input image(s) to be filtered. For supported file types see Plugin type: 2dimage/io
-o, --out-histogram=(required, output); string: output file name
--min=0; float: minimum of histogram range
--max=65535; float: maximum of histogram range
--bins=65536; ulong: number of histogram bins, set to zero to create a bin for each intensity value available in the input data. In this case the histogram range is also evaluated automatically

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the histogram over all consecutively numbered images that follow the numbering pattern inputXXXX.exr and store the output histogram in histo.txt. Use the range [0,256] and 64 bins.

mia-multihist -i input0000.exr -o histo.txt --min 0 --max 256 --bins 64

Author(s):

Gert Wollny

Prev	Up	Next
mia-3ddistance	Home	Analysis, filtering, combining, and segmentation of 3D images

│ │ │ + ...]

Description:

This program evaluates the histogram over a series of 2D images

Options:

-i, --in-file=(input, required); io: input image(s) to be filtered. For supported file types see Plugin type: 2dimage/io
-o, --out-histogram=(output, required); string: output file name
--min=0; float: minimum of histogram range
--max=65535; float: maximum of histogram range
--bins=65536; ulong: number of histogram bins, set to zero to create a bin for each intensity value available in the input data. In this case the histogram range is also evaluated automatically

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the histogram over all consecutively numbered images that follow the numbering pattern inputXXXX.exr and store the output histogram in histo.txt. Use the range [0,256] and 64 bins.

mia-multihist -i input0000.exr -o histo.txt --min 0 --max 256 --bins 64

Author(s):

Gert Wollny

Prev	Up	Next
mia-3ddistance	Home	Analysis, filtering, combining, and segmentation of 3D images

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmiamyowavelettest.html │ │ │ @@ -1,4 +1,4 @@ │ │ │ mia-myowavelettest

mia-myowavelettest
Prev	Miscellaneous programs	Next

mia-myowavelettest

Sysnopis:

mia-myowavelettest {-i string} [ │ │ │ options │ │ │ - ...]

Description:

This program runs the wavelet based slope-statistics on the mixing matrix of a ICA perfusion series.

Options:

File-IO

-i, --in-file=(required, input); string: input data set

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

│ │ │ + ...]

Description:

This program runs the wavelet based slope-statistics on the mixing matrix of a ICA perfusion series.

Options:

File-IO

-i, --in-file=(input, required); string: input data set

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

│ │ │

mia-myowavelettest

Author(s):

Gert Wollny

Prev	Up	Next
mia-labelsort	Home	mia-wavelettrans

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmiaraw2image.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-raw2image

mia-raw2image
Prev	Image conversion	Next

mia-raw2image

Sysnopis:

mia-raw2image {-i string} {-o io} {-s 2dbounds} [ │ │ │ options │ │ │ - ...]

Description:

This program is used to convert raw data to a 2D file format.

Options:

-i, --in-file=(required, input); string

input file name

-o, --out-file=(required, output); io

output file name. For supported file types see Plugin type: 2dimage/io

-r, --repn=ubyte; dict

input pixel type

bit:	binary data
sbyte:	signed 8 bit
ubyte:	unsigned 8 bit
sshort:	signed 16 bit
ushort:	unsigned 16 bit
sint:	signed 32 bit
uint:	unsigned 32 bit
slong:	signed 64 bit
ulong:	unsigned 64 bit
float:	floating point 32 bit
double:	floating point 64 bit
none:	no pixel type defined

-b, --big-endian

input data is big endian

-f, --scale=[1,1]; 2dfvector

scale of input pixels <FX,FY>

-s, --size=(required); 2dbounds

size of input <NX,NY>

-k, --skip=0; ulong

skip number of bytes from beginning of file

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Convert a data set data.raw of size <10,20> of short integer data with a pixel size of <1.2, 2.3> to a PNG file image.png

mia-raw2image -i data.raw -o image.png -s '<10,20>' -k '<1.2,2.3>' -r ushort

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dimageselect	Home	mia-raw2volume

│ │ │ + ...]

Description:

This program is used to convert raw data to a 2D file format.

Options:

-i, --in-file=(input, required); string

input file name

-o, --out-file=(output, required); io

output file name. For supported file types see Plugin type: 2dimage/io

-r, --repn=ubyte; dict

input pixel type

bit:	binary data
sbyte:	signed 8 bit
ubyte:	unsigned 8 bit
sshort:	signed 16 bit
ushort:	unsigned 16 bit
sint:	signed 32 bit
uint:	unsigned 32 bit
slong:	signed 64 bit
ulong:	unsigned 64 bit
float:	floating point 32 bit
double:	floating point 64 bit
none:	no pixel type defined

-b, --big-endian

input data is big endian

-f, --scale=[1,1]; 2dfvector

scale of input pixels <FX,FY>

-s, --size=(required); 2dbounds

size of input <NX,NY>

-k, --skip=0; ulong

skip number of bytes from beginning of file

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Convert a data set data.raw of size <10,20> of short integer data with a pixel size of <1.2, 2.3> to a PNG file image.png

mia-raw2image -i data.raw -o image.png -s '<10,20>' -k '<1.2,2.3>' -r ushort

Author(s):

Gert Wollny

Prev	Up	Next
mia-3dimageselect	Home	mia-raw2volume

│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmiaraw2volume.html │ │ │ @@ -1,3 +1,3 @@ │ │ │ mia-raw2volume

mia-raw2volume
Prev	Image conversion	Next

mia-raw2volume

Sysnopis:

mia-raw2volume {-i string} {-o io} {-s 3dbounds} [ │ │ │ options │ │ │ - ...]

Description:

This program is used to convert raw data into 3D images with apropriate metadata.

Options:

-i, --in-file=(required, input); string

input file name

-o, --out-file=(required, output); io

output file name. For supported file types see Plugin type: 3dimage/io

-r, --repn=ubyte; dict

input pixel type

bit:	binary data
sbyte:	signed 8 bit
ubyte:	unsigned 8 bit
sshort:	signed 16 bit
ushort:	unsigned 16 bit
sint:	signed 32 bit
uint:	unsigned 32 bit
slong:	signed 64 bit
ulong:	unsigned 64 bit
float:	floating point 32 bit
double:	floating point 64 bit
none:	no pixel type defined

-b, --big-endian

input data is big endian

-f, --scale=[1,1,1]; 3dfvector

scale of input voxels <FX,FY,FZ>

-k, --skip=0; ulong

skip number of bytes from beginning of file

-s, --size=(required); 3dbounds

size of input <NX,NY,NZ>

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

pixel size of <1.2, 2.3, 3.4> to an Analyze file image.hdr

mia-raw2volume -i data.raw -o image.hdr -s "<10,20,30>" -k "<1.2,2.3,3.4>" -r ushort

Author(s):

Gert Wollny

Prev	Up	Next
mia-raw2image	Home	Analysis, filtering, combining, and segmentation of 2D images

│ │ │ + ...]

Description:

This program is used to convert raw data into 3D images with apropriate metadata.

Options:

-i, --in-file=(input, required); string

input file name

-o, --out-file=(output, required); io

output file name. For supported file types see Plugin type: 3dimage/io

-r, --repn=ubyte; dict

input pixel type

bit:	binary data
sbyte:	signed 8 bit
ubyte:	unsigned 8 bit
sshort:	signed 16 bit
ushort:	unsigned 16 bit
sint:	signed 32 bit
uint:	unsigned 32 bit
slong:	signed 64 bit
ulong:	unsigned 64 bit
float:	floating point 32 bit
double:	floating point 64 bit
none:	no pixel type defined

-b, --big-endian

input data is big endian

-f, --scale=[1,1,1]; 3dfvector

scale of input voxels <FX,FY,FZ>

-k, --skip=0; ulong

skip number of bytes from beginning of file

-s, --size=(required); 3dbounds

size of input <NX,NY,NZ>

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

pixel size of <1.2, 2.3, 3.4> to an Analyze file image.hdr

mia-raw2volume -i data.raw -o image.hdr -s "<10,20,30>" -k "<1.2,2.3,3.4>" -r ushort

Author(s):

Gert Wollny

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│ │ ├── ./usr/share/doc/mia-2.4/userref/Secmiawavelettrans.html │ │ │ @@ -1,4 +1,4 @@ │ │ │ mia-wavelettrans

mia-wavelettrans
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mia-wavelettrans

Sysnopis:

mia-wavelettrans {-i string} {-o string} [ │ │ │ options │ │ │ - ...]

Description:

This program runs the a column-wise discret wavelet forward transform on the data given by an input text file.

Options:

File-IO

-i, --in-file=(required, input); string: input data set
-o, --out-file=(required, output); string: output data set
-s, --save-wave=(output); string: base name of the output files that will store the wavelet coefficients as matrix

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Wavelet

-w, --wavelet=c-daubechies; dict

wavelet to be used

haar:	HAAR wavelet
c-haar:	HAAR wavelet (centered)
daubechies:	Daubechies wavelet
c-daubechies:	Daubechies wavelet (centered)
bspline:	B-Spline wavelet
c-bspline:	B-Spline wavelet (centered)

-m, --member=10; int

wavelet member ID

Example:

│ │ │ + ...]

Description:

This program runs the a column-wise discret wavelet forward transform on the data given by an input text file.

Options:

File-IO

-i, --in-file=(input, required); string: input data set
-o, --out-file=(output, required); string: output data set
-s, --save-wave=(output); string: base name of the output files that will store the wavelet coefficients as matrix

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:	Function call trace
debug:	Debug output
info:	Low level messages
message:	Normal messages
warning:	Warnings
fail:	Report test failures
error:	Report errors
fatal:	Report only fatal errors

--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int: Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Wavelet

-w, --wavelet=c-daubechies; dict

wavelet to be used

haar:	HAAR wavelet
c-haar:	HAAR wavelet (centered)
daubechies:	Daubechies wavelet
c-daubechies:	Daubechies wavelet (centered)
bspline:	B-Spline wavelet
c-bspline:	B-Spline wavelet (centered)

-m, --member=10; int

wavelet member ID

Example:

│ │ │

mia-wavelettrans

Author(s):

Gert Wollny

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mia-myowavelettest	Home	Creation, analysis, and filtering of triangular 3D meshes