--- /tmp/mia-2.4.7-71i6qbm0u/debian/mia-tools_2.4.7-7_amd64.deb +++ mia-tools_2.4.7-7_amd64.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 7532 2021-01-11 21:49:29.000000 control.tar.xz │ --rw-r--r-- 0 0 0 1933796 2021-01-11 21:49:29.000000 data.tar.xz │ +-rw-r--r-- 0 0 0 7516 2021-01-11 21:49:29.000000 control.tar.xz │ +-rw-r--r-- 0 0 0 1933940 2021-01-11 21:49:29.000000 data.tar.xz ├── control.tar.xz │ ├── control.tar │ │ ├── ./md5sums │ │ │ ├── ./md5sums │ │ │ │┄ Files differ ├── data.tar.xz │ ├── data.tar │ │ ├── file list │ │ │ @@ -143,142 +143,142 @@ │ │ │ -rw-r--r-- 0 root (0) root (0) 10430 2020-04-26 10:42:08.000000 ./usr/share/doc/mia-tools/changelog.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1127 2021-01-11 21:49:29.000000 ./usr/share/doc/mia-tools/copyright │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2021-01-11 21:49:29.000000 ./usr/share/lintian/ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2021-01-11 21:49:29.000000 ./usr/share/lintian/overrides/ │ │ │ -rw-r--r-- 0 root (0) root (0) 425 2021-01-11 21:49:29.000000 ./usr/share/lintian/overrides/mia-tools │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2021-01-11 21:49:29.000000 ./usr/share/man/ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2021-01-11 21:49:29.000000 ./usr/share/man/man1/ │ │ │ --rw-r--r-- 0 root (0) root (0) 1472 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2davgmasked.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1566 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dbinarycombine.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1474 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2davgmasked.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1565 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dbinarycombine.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 2633 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dcost.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1749 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2ddeform.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1695 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2ddistance.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1746 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2ddeform.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1691 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2ddistance.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1867 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2deval-transformquantity.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 3501 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dfluid-syn-registration.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1915 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dfluid.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1548 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dforce.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 3498 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dfluid-syn-registration.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1913 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dfluid.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1543 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dforce.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1810 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dfuzzysegment.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1592 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dgrayimage-combine-to-rgb.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 3457 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dgroundtruthreg.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1469 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dimagecombine-dice.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1625 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dimagecombiner.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1774 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dimagecreator.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 6177 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dimagefilter.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 6373 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dimagefilterstack.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1470 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dimagecombine-dice.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1620 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dimagecombiner.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1772 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dimagecreator.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 6179 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dimagefilter.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 6374 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dimagefilterstack.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1442 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dimagefullstats.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 5279 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dimageregistration.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 5274 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dimageregistration.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1490 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dimageselect.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1426 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dimageseries-maximum-intensity-projection.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1950 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dimagestack-cmeans.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1428 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dimageseries-maximum-intensity-projection.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1949 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dimagestack-cmeans.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1622 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dimagestats.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1669 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dlerp.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 3668 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dmany2one-nonrigid.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 2776 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dmulti-force.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 5396 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dmultiimageregistration.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 3675 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dmany2one-nonrigid.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 2777 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dmulti-force.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 5397 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dmultiimageregistration.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1856 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dmultiimageto3d.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1542 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dmultiimagevar.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1540 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dmultiimagevar.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 2193 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dmyocard-ica.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1815 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dmyocard-icaseries.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1731 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dmyocard-segment.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 6381 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dmyoica-full.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 5456 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dmyoica-nonrigid-parallel.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 5387 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dmyoica-nonrigid.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 3712 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dmyoica-nonrigid2.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 5449 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dmyoica-nonrigid-parallel.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 5394 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dmyoica-nonrigid.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 3710 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dmyoica-nonrigid2.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 6761 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dmyoicapgt.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 4509 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dmyomilles.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 5660 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dmyoperiodic-nonrigid.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 3368 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dmyopgt-nonrigid.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 5657 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dmyoperiodic-nonrigid.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 3372 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dmyopgt-nonrigid.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 5532 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dmyoserial-nonrigid.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1006 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dmyoseries-compdice.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1005 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dmyoseries-dice.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 3685 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dmyoset-all2one-nonrigid.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1005 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dmyoseries-compdice.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1006 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dmyoseries-dice.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 3690 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dmyoset-all2one-nonrigid.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 981 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dsegcompare.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 988 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dseghausdorff.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1793 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dsegment-ahmed.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1791 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dsegment-ahmed.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 6323 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dsegment-fuzzyw.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 2301 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dsegment-local-cmeans.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1902 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dsegment-local-kmeans.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1837 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dsegment-per-pixel-kmeans.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1252 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dsegmentcropbox.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1842 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dsegment-per-pixel-kmeans.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1257 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dsegmentcropbox.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1648 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dsegseriesstats.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1692 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dsegshift.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1132 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dsegshiftperslice.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1574 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dseries-mincorr.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1133 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dsegshiftperslice.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1578 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dseries-mincorr.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1511 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dseries-sectionmask.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 976 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dseries-segdistance.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 6406 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dseries2dordermedian.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1726 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dseries2sets.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1717 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dseriescorr.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 6305 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dseriesgradMAD.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 6403 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dseries2dordermedian.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1725 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dseries2sets.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1712 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dseriescorr.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 6302 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dseriesgradMAD.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1724 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dseriesgradvariation.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 993 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dserieshausdorff.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 6348 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dseriessmoothgradMAD.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1573 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dseriestovolume.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 2125 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dstack-cmeans-presegment.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 6342 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dseriessmoothgradMAD.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1574 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dseriestovolume.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 2128 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dstack-cmeans-presegment.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 6952 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dstackfilter.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1878 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dto3dimage.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1882 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dto3dimage.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1888 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dto3dimageb.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1371 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dtrackpixelmovement.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1672 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dtransform.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1117 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dtransformation-to-strain.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1630 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dbinarycombine.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1366 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dtrackpixelmovement.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1677 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dtransform.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1122 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-2dtransformation-to-strain.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1628 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dbinarycombine.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1879 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dbrainextractT1.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1739 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dcombine-imageseries.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1655 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dcombine-mr-segmentations.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 3432 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dcost-translatedgrad.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1740 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dcombine-imageseries.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1650 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dcombine-mr-segmentations.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 3428 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dcost-translatedgrad.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 6736 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dcost.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1646 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dcrispsegment.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1864 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3ddeform.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 2013 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3ddistance-stats.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1140 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3ddistance.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1875 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3deval-transformquantity.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1651 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dcrispsegment.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1869 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3ddeform.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 2014 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3ddistance-stats.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1141 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3ddistance.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1878 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3deval-transformquantity.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1670 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dfield2norm.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 3571 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dfluid-syn-registration.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 2323 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dfluid.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 2369 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dforce.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1708 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dfuzzysegment.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1469 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dgetsize.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 2199 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dgetslice.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 3570 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dfluid-syn-registration.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 2318 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dfluid.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 2368 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dforce.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1706 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dfuzzysegment.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1468 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dgetsize.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 2200 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dgetslice.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1968 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dimageaddattributes.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1658 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dimagecombine.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1906 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dimagecreator.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 5703 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dimagefilter.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1907 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dimagecreator.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 5696 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dimagefilter.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 5897 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dimagefilterstack.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1548 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dimageselect.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1543 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dimageselect.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1934 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dimagestatistics-in-mask.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1545 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dimagestats.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1269 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3disosurface-from-stack.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 2262 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3disosurface-from-volume.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1140 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dlandmarks-distances.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1299 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dlandmarks-transform.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1304 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dlandmarks-transform.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1719 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dlerp.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 7897 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dmany2one-nonrigid.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 7896 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dmany2one-nonrigid.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1877 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dmaskseeded.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 2559 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dmotioncompica-nonrigid.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 9543 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dnonrigidreg-alt.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 9401 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dnonrigidreg.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 10016 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dprealign-nonrigid.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 2562 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dmotioncompica-nonrigid.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 9541 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dnonrigidreg-alt.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 9404 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dnonrigidreg.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 10024 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dprealign-nonrigid.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 5803 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dpropose-boundingbox.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 5107 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3drigidreg.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 5113 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3drigidreg.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1936 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dsegment-ahmed.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 2573 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dsegment-local-cmeans.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 9444 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dserial-nonrigid.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1585 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dseries-track-intensity.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1375 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dtrackpixelmovement.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1714 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dtransform.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 2568 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dsegment-local-cmeans.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 9440 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dserial-nonrigid.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1590 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dseries-track-intensity.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1368 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dtrackpixelmovement.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1718 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dtransform.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1314 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dtransform2vf.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1267 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dvectorfieldcreate.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1657 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dvf2transform.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1661 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dvf2transform.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1268 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-3dvfcompare.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1126 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-cmeans.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 883 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-filenumberpattern.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 991 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-labelsort.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 6457 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-mesh-deformable-model.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 2139 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-mesh-to-maskimage.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1121 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-cmeans.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 882 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-filenumberpattern.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 986 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-labelsort.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 6458 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-mesh-deformable-model.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 2140 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-mesh-to-maskimage.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1955 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-meshdistance-to-stackmask.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 2433 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-meshfilter.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1656 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-multihist.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 2435 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-meshfilter.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1659 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-multihist.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 901 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-myowavelettest.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 850 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-plugin-help.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1736 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-raw2image.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1737 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-raw2image.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1801 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-raw2volume.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1090 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-wavelettrans.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1086 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-wavelettrans.1.gz │ │ ├── ./usr/share/man/man1/mia-2davgmasked.1.gz │ │ │ ├── mia-2davgmasked.1 │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2davgmasked \-i \-m [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2davgmasked │ │ │ │ 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. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-files=(input, required); io" │ │ │ │ +.IP "\-i \-\-in-files=(required, input); io" │ │ │ │ input image(s) │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-m \-\-mask-file=(input, required); io" │ │ │ │ +.IP "\-m \-\-mask-file=(required, input); io" │ │ │ │ mask image, must be of type byte │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ │ │ .RS │ │ │ │ .IP "\-V \-\-verbose=warning" │ │ │ │ verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are: │ │ ├── ./usr/share/man/man1/mia-2dbinarycombine.1.gz │ │ │ ├── mia-2dbinarycombine.1 │ │ │ │ @@ -5,21 +5,21 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dbinarycombine \-1 \-2 \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dbinarycombine │ │ │ │ This program is used to combine two binary images by some kind of operation. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-1 \-\-file1=(required, input); io" │ │ │ │ +.IP "\-1 \-\-file1=(input, required); io" │ │ │ │ input mask image 1 │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-2 \-\-file2=(required, input); io" │ │ │ │ +.IP "\-2 \-\-file2=(input, required); io" │ │ │ │ input mask image 2 │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ output mask image │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-p \-\-operation=nor" │ │ │ │ Operation to be applied │ │ │ │ │ │ │ │ .RS 10 │ │ │ │ .I │ │ ├── ./usr/share/man/man1/mia-2ddeform.1.gz │ │ │ ├── mia-2ddeform.1 │ │ │ │ @@ -8,15 +8,15 @@ │ │ │ │ .B mia\-2ddeform │ │ │ │ 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)' │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-in-file=(required, input); io" │ │ │ │ input image │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ transformed image │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-t \-\-transformation=(required, input); io" │ │ │ │ transformation vector field │ │ │ │ For supported file types see PLUGINS:2dvf/io │ │ │ │ .IP "\-p \-\-interpolator=bspline:d=3" │ │ │ │ image interpolator kernel │ │ ├── ./usr/share/man/man1/mia-2ddistance.1.gz │ │ │ ├── mia-2ddistance.1 │ │ │ │ @@ -11,15 +11,15 @@ │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-in-file=(required, input); io" │ │ │ │ input image │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-d \-\-distance-file=(required, input); io" │ │ │ │ distance field image (floating point) │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-o \-\-out-file=(output, required); string" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); string" │ │ │ │ output file, '\-': write to stdout │ │ │ │ │ │ │ │ .IP "\-s \-\-scale=1" │ │ │ │ distance scaling factor │ │ │ │ │ │ │ │ .IP "\-m \-\-method=avg" │ │ │ │ distance measuring method │ │ ├── ./usr/share/man/man1/mia-2dfluid-syn-registration.1.gz │ │ │ ├── mia-2dfluid-syn-registration.1 │ │ │ │ @@ -64,18 +64,18 @@ │ │ │ │ │ │ │ │ .IP " \-\-version" │ │ │ │ print the version number and exit │ │ │ │ │ │ │ │ .RE │ │ │ │ .SS IO │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-image=(required, input); io" │ │ │ │ +.IP "\-i \-\-in-image=(input, required); io" │ │ │ │ test image │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-r \-\-ref-image=(required, input); io" │ │ │ │ +.IP "\-r \-\-ref-image=(input, required); io" │ │ │ │ reference image │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-o \-\-transform=(output, required); io" │ │ │ │ output transformation │ │ │ │ For supported file types see PLUGINS:2dtransform/io │ │ │ │ .IP "\-O \-\-inverse-transform=(output, required); io" │ │ │ │ inverse output transformation │ │ ├── ./usr/share/man/man1/mia-2dfluid.1.gz │ │ │ ├── mia-2dfluid.1 │ │ │ │ @@ -14,18 +14,18 @@ │ │ │ │ .UE │ │ │ │ .RE │ │ │ │ │ │ │ │ It uses SSD as the sole registration criterion. │ │ │ │ .SH OPTIONS │ │ │ │ .SS File-IO │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-image=(input, required); io" │ │ │ │ +.IP "\-i \-\-in-image=(required, input); io" │ │ │ │ input (test) image to be registered │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-r \-\-ref-image=(input, required); io" │ │ │ │ +.IP "\-r \-\-ref-image=(required, input); io" │ │ │ │ reference image │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-o \-\-out-transformation=(output); io" │ │ │ │ output transformation comprising the registration │ │ │ │ For supported file types see PLUGINS:2dvf/io │ │ │ │ .IP "\-d \-\-out-image=(output); io" │ │ │ │ output image deformed according to the transformation │ │ ├── ./usr/share/man/man1/mia-2dforce.1.gz │ │ │ ├── mia-2dforce.1 │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dforce \-i \-r \-o \-c [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dforce │ │ │ │ This image evaluate the force field between two images based on a given cost function. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-src-file=(input, required); io" │ │ │ │ +.IP "\-i \-\-src-file=(required, input); io" │ │ │ │ input image │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-r \-\-ref-file=(input, required); io" │ │ │ │ +.IP "\-r \-\-ref-file=(required, input); io" │ │ │ │ reference image │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-o \-\-out-file=(required, output); io" │ │ │ │ output force norm image │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-c \-\-cost=(required); string" │ │ │ │ cost function to use │ │ ├── ./usr/share/man/man1/mia-2dgroundtruthreg.1.gz │ │ │ ├── mia-2dgroundtruthreg.1 │ │ │ │ @@ -15,18 +15,18 @@ │ │ │ │ .RE │ │ │ │ │ │ │ │ Note that for this nonlinear motion correction a preceding linear registration step is usually required. │ │ │ │ .SH OPTIONS │ │ │ │ .SS │ │ │ │ File-IO │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ +.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ input perfusion data set │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(output, required); string" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); string" │ │ │ │ output perfusion data set │ │ │ │ │ │ │ │ .IP "\-r \-\-registered=reg" │ │ │ │ file name base for registered files │ │ │ │ │ │ │ │ .RE │ │ │ │ .SS │ │ ├── ./usr/share/man/man1/mia-2dimagecombine-dice.1.gz │ │ │ ├── mia-2dimagecombine-dice.1 │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dimagecombine\-dice \-1 \-2 [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dimagecombine\-dice │ │ │ │ This program evaluate the dice index of two binary masks given as binary images. The result is written to stdout. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-1 \-\-in-file-1=(input, required); io" │ │ │ │ +.IP "\-1 \-\-in-file-1=(required, input); io" │ │ │ │ input image 1 │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-2 \-\-in-file-2=(input, required); io" │ │ │ │ +.IP "\-2 \-\-in-file-2=(required, input); io" │ │ │ │ input image 2 │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ │ │ .RS │ │ │ │ .IP "\-V \-\-verbose=warning" │ │ │ │ verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are: │ │ ├── ./usr/share/man/man1/mia-2dimagecombiner.1.gz │ │ │ ├── mia-2dimagecombiner.1 │ │ │ │ @@ -11,15 +11,15 @@ │ │ │ │ .RS │ │ │ │ .IP "\-1 \-\-in-file-1=(input, required); io" │ │ │ │ first input image to be combined │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-2 \-\-in-file-2=(input, required); io" │ │ │ │ second input image to be combined │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ output image(s) that have been filtered │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-p \-\-operation=absdiff" │ │ │ │ operation to be applied │ │ │ │ For supported plugins see PLUGINS:2dimage/combiner │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ ├── ./usr/share/man/man1/mia-2dimagecreator.1.gz │ │ │ ├── mia-2dimagecreator.1 │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dimagecreator \-o \-j [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dimagecreator │ │ │ │ This program is used to create test images. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ output file for create object │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-s \-\-size=[128,128]" │ │ │ │ size of the object │ │ │ │ │ │ │ │ .IP "\-r \-\-repn=ubyte" │ │ │ │ input pixel type │ │ ├── ./usr/share/man/man1/mia-2dimagefilter.1.gz │ │ │ ├── mia-2dimagefilter.1 │ │ │ │ @@ -7,18 +7,18 @@ │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dimagefilter │ │ │ │ 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 │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ input image(s) to be filtered │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ output image(s) that have been filtered │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ │ │ .RS │ │ │ │ .IP "\-V \-\-verbose=warning" │ │ │ │ verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are: │ │ │ │ @@ -348,15 +348,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B 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: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ image │ │ │ │ -=(required, input, io) │ │ │ │ +=(input, required, io) │ │ │ │ .RS 2 │ │ │ │ second image that is needed in the combiner. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ @@ -692,15 +692,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B labelmap │ │ │ │ Image filter to remap label id's. Only applicable to images with integer valued intensities/labels., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ map │ │ │ │ -=(required, input, string) │ │ │ │ +=(input, required, string) │ │ │ │ .RS 2 │ │ │ │ Label mapping file. │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ .B labelscale │ │ │ │ @@ -718,15 +718,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B load │ │ │ │ Load the input image from a file and use it to replace the current image in the pipeline., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ file │ │ │ │ -=(required, input, io) │ │ │ │ +=(input, required, io) │ │ │ │ .RS 2 │ │ │ │ name of the input file to load from.. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ @@ -757,15 +757,15 @@ │ │ │ │ .RE │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ input │ │ │ │ -=(required, input, io) │ │ │ │ +=(input, required, io) │ │ │ │ .RS 2 │ │ │ │ second input image file name. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ @@ -780,25 +780,25 @@ │ │ │ │ .TP 10 │ │ │ │ .B maxflow │ │ │ │ This filter implements the uses the max-flow min-cut algorithmfor image segmentation, supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ sink-flow │ │ │ │ -=(required, input, io) │ │ │ │ +=(input, required, io) │ │ │ │ .RS 2 │ │ │ │ Image of float type to define the per\-pixel flow to the sink. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ source-flow │ │ │ │ -=(required, input, io) │ │ │ │ +=(input, required, io) │ │ │ │ .RS 2 │ │ │ │ Image of float type to define the per\-pixel flow to the source. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ @@ -826,15 +826,15 @@ │ │ │ │ Intensity thresholding parameter: Pixels with intensities below this threshold will be set to zero, and also not used when evaluating mean and variation. │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ varfile │ │ │ │ -=(required, output, io) │ │ │ │ +=(output, required, io) │ │ │ │ .RS 2 │ │ │ │ name of the output file to save the variation image too.. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ @@ -862,15 +862,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B 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: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ madfile │ │ │ │ -=(required, output, io) │ │ │ │ +=(output, required, io) │ │ │ │ .RS 2 │ │ │ │ name of the output file to save the median absolute deviation image too.. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ @@ -987,15 +987,15 @@ │ │ │ │ For supported plug-ins see PLUGINS:2dimage/shape │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ seed │ │ │ │ -=(required, input, io) │ │ │ │ +=(input, required, io) │ │ │ │ .RS 2 │ │ │ │ seed image (bit valued). │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ @@ -1168,28 +1168,28 @@ │ │ │ │ For supported plug-ins see PLUGINS:2dimage/shape │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ seed │ │ │ │ -=(required, input, string) │ │ │ │ +=(input, required, string) │ │ │ │ .RS 2 │ │ │ │ seed input image containing the lables for the initial regions. │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ .B tee │ │ │ │ Save the input image to a file and also pass it through to the next filter, supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ file │ │ │ │ -=(required, output, io) │ │ │ │ +=(output, required, io) │ │ │ │ .RS 2 │ │ │ │ name of the output file to save the image too.. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ @@ -1253,15 +1253,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B transform │ │ │ │ Transform the input image with the given transformation., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ file │ │ │ │ -=(required, input, io) │ │ │ │ +=(input, required, io) │ │ │ │ .RS 2 │ │ │ │ Name of the file containing the transformation.. │ │ │ │ For supported file types see PLUGINS:2dtransform/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ ├── ./usr/share/man/man1/mia-2dimagefilterstack.1.gz │ │ │ ├── mia-2dimagefilterstack.1 │ │ │ │ @@ -6,15 +6,15 @@ │ │ │ │ .B mia\-2dimagefilterstack \-i \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dimagefilterstack │ │ │ │ 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. │ │ │ │ .SH OPTIONS │ │ │ │ .SS File IO │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ +.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ input image(s) to be filtered │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-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 PLUGINS:2dimage/io │ │ │ │ .IP "\-t \-\-type=" │ │ │ │ output file type, if not given the input type is used │ │ │ │ @@ -388,15 +388,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B 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: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ image │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ second image that is needed in the combiner. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ @@ -732,15 +732,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B labelmap │ │ │ │ Image filter to remap label id's. Only applicable to images with integer valued intensities/labels., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ map │ │ │ │ -=(input, required, string) │ │ │ │ +=(required, input, string) │ │ │ │ .RS 2 │ │ │ │ Label mapping file. │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ .B labelscale │ │ │ │ @@ -758,15 +758,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B load │ │ │ │ Load the input image from a file and use it to replace the current image in the pipeline., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ file │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ name of the input file to load from.. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ @@ -797,15 +797,15 @@ │ │ │ │ .RE │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ input │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ second input image file name. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ @@ -820,25 +820,25 @@ │ │ │ │ .TP 10 │ │ │ │ .B maxflow │ │ │ │ This filter implements the uses the max-flow min-cut algorithmfor image segmentation, supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ sink-flow │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ Image of float type to define the per\-pixel flow to the sink. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ source-flow │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ Image of float type to define the per\-pixel flow to the source. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ @@ -1027,15 +1027,15 @@ │ │ │ │ For supported plug-ins see PLUGINS:2dimage/shape │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ seed │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ seed image (bit valued). │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ @@ -1208,15 +1208,15 @@ │ │ │ │ For supported plug-ins see PLUGINS:2dimage/shape │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ seed │ │ │ │ -=(input, required, string) │ │ │ │ +=(required, input, string) │ │ │ │ .RS 2 │ │ │ │ seed input image containing the lables for the initial regions. │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ .B tee │ │ │ │ @@ -1293,15 +1293,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B transform │ │ │ │ Transform the input image with the given transformation., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ file │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ Name of the file containing the transformation.. │ │ │ │ For supported file types see PLUGINS:2dtransform/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ ├── ./usr/share/man/man1/mia-2dimagefullstats.1.gz │ │ │ ├── mia-2dimagefullstats.1 │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dimagefullstats \-i [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dimagefullstats │ │ │ │ This progranm is used to evaluate some statistics of an image. Output is Mean, Variation, Median, Min and Max of the intensity values. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ input image │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ │ │ .RS │ │ │ │ .IP "\-V \-\-verbose=warning" │ │ │ │ verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are: │ │ ├── ./usr/share/man/man1/mia-2dimageregistration.1.gz │ │ │ ├── mia-2dimageregistration.1 │ │ │ │ @@ -15,15 +15,15 @@ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-r \-\-ref-image=(input, required); io" │ │ │ │ reference image to be registered to │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-o \-\-out-image=(output); io" │ │ │ │ registered output image │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-t \-\-transformation=(required, output); io" │ │ │ │ +.IP "\-t \-\-transformation=(output, required); io" │ │ │ │ output transformation comprising the registration │ │ │ │ For supported file types see PLUGINS:2dtransform/io │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ │ │ .RS │ │ │ │ .IP "\-V \-\-verbose=warning" │ │ │ │ verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are: │ │ ├── ./usr/share/man/man1/mia-2dimageseries-maximum-intensity-projection.1.gz │ │ │ ├── mia-2dimageseries-maximum-intensity-projection.1 │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dimageseries\-maximum\-intensity\-projection \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dimageseries\-maximum\-intensity\-projection │ │ │ │ This program is used to evaluate the per-pixel maximum intensity of an image series. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ output image │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ │ │ .RS │ │ │ │ .IP "\-V \-\-verbose=warning" │ │ │ │ verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are: │ │ ├── ./usr/share/man/man1/mia-2dimagestack-cmeans.1.gz │ │ │ ├── mia-2dimagestack-cmeans.1 │ │ │ │ @@ -6,15 +6,15 @@ │ │ │ │ .B mia\-2dimagestack\-cmeans \-i \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dimagestack\-cmeans │ │ │ │ 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 │ │ │ │ .SH OPTIONS │ │ │ │ .SS File-IO │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ input image(s) to be filtered │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-o \-\-out-probmap=(output, required); string" │ │ │ │ Save probability map to this file │ │ │ │ │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ ├── ./usr/share/man/man1/mia-2dimagestats.1.gz │ │ │ ├── mia-2dimagestats.1 │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dimagestats \-i [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dimagestats │ │ │ │ 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 │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ input image to be analyzed │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-t \-\-thresh=10" │ │ │ │ intensity thresh to ignore │ │ │ │ │ │ │ │ .IP "\-g \-\-high-thresh=0.05" │ │ │ │ upper histogram percentage to ignore │ │ ├── ./usr/share/man/man1/mia-2dlerp.1.gz │ │ │ ├── mia-2dlerp.1 │ │ │ │ @@ -5,21 +5,21 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dlerp \-1 \-2 \-o \-p [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dlerp │ │ │ │ Merge two images by pixel-wise linearly combining their intensities. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-1 \-\-first=(required, input); io" │ │ │ │ +.IP "\-1 \-\-first=(input, required); io" │ │ │ │ first input image │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-2 \-\-second=(required, input); io" │ │ │ │ +.IP "\-2 \-\-second=(input, required); io" │ │ │ │ second input image │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ output vector field │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-p \-\-positions=(required); vfloat" │ │ │ │ image series positions (first, target, second) │ │ │ │ │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ ├── ./usr/share/man/man1/mia-2dmany2one-nonrigid.1.gz │ │ │ ├── mia-2dmany2one-nonrigid.1 │ │ │ │ @@ -7,15 +7,15 @@ │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dmany2one\-nonrigid │ │ │ │ This program registers all images of a conscutively numbered set of images to one common user defined reference. │ │ │ │ .SH OPTIONS │ │ │ │ .SS │ │ │ │ File-IO │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ +.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ input perfusion data set │ │ │ │ │ │ │ │ .IP "\-o \-\-out-file=(output, required); string" │ │ │ │ file name for registered images, numbering and pattern are deducted from the input data │ │ │ │ │ │ │ │ .RE │ │ │ │ .SS │ │ ├── ./usr/share/man/man1/mia-2dmulti-force.1.gz │ │ │ ├── mia-2dmulti-force.1 │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dmulti\-force \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dmulti\-force │ │ │ │ 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). │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ output norm image │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ │ │ .RS │ │ │ │ .IP "\-V \-\-verbose=warning" │ │ │ │ verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are: │ │ ├── ./usr/share/man/man1/mia-2dmultiimageregistration.1.gz │ │ │ ├── mia-2dmultiimageregistration.1 │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dmultiimageregistration \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dmultiimageregistration │ │ │ │ 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) │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-o \-\-out-transform=(output, required); io" │ │ │ │ +.IP "\-o \-\-out-transform=(required, output); io" │ │ │ │ output transformation │ │ │ │ For supported file types see PLUGINS:2dtransform/io │ │ │ │ .IP "\-l \-\-levels=3" │ │ │ │ multi\-resolution levels │ │ │ │ │ │ │ │ .IP "\-O \-\-optimizer=gsl:opt=gd,step=0.1" │ │ │ │ Optimizer used for minimization │ │ ├── ./usr/share/man/man1/mia-2dmultiimagevar.1.gz │ │ │ ├── mia-2dmultiimagevar.1 │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dmultiimagevar \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dmultiimagevar │ │ │ │ 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. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ output image │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ │ │ .RS │ │ │ │ .IP "\-V \-\-verbose=warning" │ │ │ │ verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are: │ │ ├── ./usr/share/man/man1/mia-2dmyoica-nonrigid-parallel.1.gz │ │ │ ├── mia-2dmyoica-nonrigid-parallel.1 │ │ │ │ @@ -14,15 +14,15 @@ │ │ │ │ .UE │ │ │ │ .RE │ │ │ │ │ │ │ │ This version of the program runs all registrations in parallel. │ │ │ │ .SH OPTIONS │ │ │ │ .SS File-IO │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ input perfusion data set │ │ │ │ │ │ │ │ .IP "\-o \-\-out-file=(output, required); string" │ │ │ │ output perfusion data set │ │ │ │ │ │ │ │ .IP "\-r \-\-registered=reg" │ │ │ │ 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. │ │ ├── ./usr/share/man/man1/mia-2dmyoica-nonrigid.1.gz │ │ │ ├── mia-2dmyoica-nonrigid.1 │ │ │ │ @@ -13,15 +13,15 @@ │ │ │ │ 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. │ │ │ │ .UE │ │ │ │ .RE │ │ │ │ │ │ │ │ .SH OPTIONS │ │ │ │ .SS File-IO │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ +.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ input perfusion data set │ │ │ │ │ │ │ │ .IP "\-o \-\-out-file=(output, required); string" │ │ │ │ output perfusion data set │ │ │ │ │ │ │ │ .IP "\-r \-\-registered=reg" │ │ │ │ file name base for registered fiels │ │ ├── ./usr/share/man/man1/mia-2dmyoica-nonrigid2.1.gz │ │ │ ├── mia-2dmyoica-nonrigid2.1 │ │ │ │ @@ -8,18 +8,18 @@ │ │ │ │ .B mia\-2dmyoica\-nonrigid2 │ │ │ │ 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. │ │ │ │ .SH OPTIONS │ │ │ │ .SS │ │ │ │ File-IO │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ +.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ input perfusion data set │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(output, required); string" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); string" │ │ │ │ output perfusion data set │ │ │ │ │ │ │ │ .IP "\-r \-\-registered=reg" │ │ │ │ file name base for registered fiels │ │ │ │ │ │ │ │ .IP " \-\-save-cropped=" │ │ │ │ save cropped set to this file │ │ ├── ./usr/share/man/man1/mia-2dmyoperiodic-nonrigid.1.gz │ │ │ ├── mia-2dmyoperiodic-nonrigid.1 │ │ │ │ @@ -14,15 +14,15 @@ │ │ │ │ .UE │ │ │ │ .RE │ │ │ │ │ │ │ │ .SH OPTIONS │ │ │ │ .SS │ │ │ │ File-IO │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ +.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ input perfusion data set │ │ │ │ │ │ │ │ .IP "\-o \-\-out-file=(required, output); string" │ │ │ │ output perfusion data set │ │ │ │ │ │ │ │ .IP "\-r \-\-registered=reg" │ │ │ │ file name base for registered fiels │ │ ├── ./usr/share/man/man1/mia-2dmyopgt-nonrigid.1.gz │ │ │ ├── mia-2dmyopgt-nonrigid.1 │ │ │ │ @@ -18,15 +18,15 @@ │ │ │ │ .SH OPTIONS │ │ │ │ .SS │ │ │ │ File-IO │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-in-file=(required, input); string" │ │ │ │ input perfusion data set │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(required, output); string" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); string" │ │ │ │ output perfusion data set │ │ │ │ │ │ │ │ .IP "\-r \-\-registered=reg" │ │ │ │ file name base for registered files, the image file type is the same as given in the input data set │ │ │ │ │ │ │ │ .RE │ │ │ │ .SS │ │ ├── ./usr/share/man/man1/mia-2dmyoseries-compdice.1.gz │ │ │ ├── mia-2dmyoseries-compdice.1 │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dmyoseries\-compdice \-1 \-2 [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dmyoseries\-compdice │ │ │ │ This program is used to evaluate the per-frame dice index of segmented regions of two image series │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-1 \-\-first=(required, input); string" │ │ │ │ +.IP "\-1 \-\-first=(input, required); string" │ │ │ │ first segmentation set │ │ │ │ │ │ │ │ -.IP "\-2 \-\-second=(required, input); string" │ │ │ │ +.IP "\-2 \-\-second=(input, required); string" │ │ │ │ second segmentation set │ │ │ │ │ │ │ │ .IP "\-k \-\-skip=2" │ │ │ │ images to skip atthe begin of the series │ │ │ │ │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ ├── ./usr/share/man/man1/mia-2dmyoseries-dice.1.gz │ │ │ ├── mia-2dmyoseries-dice.1 │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dmyoseries\-dice \-i [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dmyoseries\-dice │ │ │ │ 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. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-input=(input, required); string" │ │ │ │ +.IP "\-i \-\-input=(required, input); string" │ │ │ │ original segmentation set │ │ │ │ │ │ │ │ .IP "\-k \-\-skip=2" │ │ │ │ images to skip atthe bgin of the series │ │ │ │ │ │ │ │ .IP "\-r \-\-reference=20" │ │ │ │ reference image │ │ ├── ./usr/share/man/man1/mia-2dmyoset-all2one-nonrigid.1.gz │ │ │ ├── mia-2dmyoset-all2one-nonrigid.1 │ │ │ │ @@ -7,18 +7,18 @@ │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dmyoset\-all2one\-nonrigid │ │ │ │ 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. │ │ │ │ .SH OPTIONS │ │ │ │ .SS │ │ │ │ File-IO │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ +.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ input perfusion data set │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(output, required); string" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); string" │ │ │ │ output perfusion data set │ │ │ │ │ │ │ │ .IP " \-\-out-filebase=reg" │ │ │ │ file name basae for registered files, file type is deducted from the image file type in the input data set. │ │ │ │ │ │ │ │ .RE │ │ │ │ .SS │ │ ├── ./usr/share/man/man1/mia-2dsegment-ahmed.1.gz │ │ │ ├── mia-2dsegment-ahmed.1 │ │ │ │ @@ -13,18 +13,18 @@ │ │ │ │ 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, │ │ │ │ .UE │ │ │ │ .RE │ │ │ │ │ │ │ │ changes are: p=2, and exp │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ image to be segmented │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ +.IP "\-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 PLUGINS:2dimage/io │ │ │ │ .IP "\-a \-\-no-of-classes=3" │ │ │ │ number of classes │ │ │ │ │ │ │ │ .IP "\-b \-\-bias-correct" │ │ │ │ apply bias field correction │ │ ├── ./usr/share/man/man1/mia-2dsegment-per-pixel-kmeans.1.gz │ │ │ ├── mia-2dsegment-per-pixel-kmeans.1 │ │ │ │ @@ -6,15 +6,15 @@ │ │ │ │ .B mia\-2dsegment\-per\-pixel\-kmeans \-i \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dsegment\-per\-pixel\-kmeans │ │ │ │ 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. │ │ │ │ .SH OPTIONS │ │ │ │ .SS File-IO │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ +.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ image to be segmented │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-o \-\-out-file=(output, required); io" │ │ │ │ class label image based on merging local labels │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ ├── ./usr/share/man/man1/mia-2dsegmentcropbox.1.gz │ │ │ ├── mia-2dsegmentcropbox.1 │ │ │ │ @@ -11,15 +11,15 @@ │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-in-file=(input, required); string" │ │ │ │ input segmentation set │ │ │ │ │ │ │ │ .IP "\-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 │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(output, required); string" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); string" │ │ │ │ output segmentation set │ │ │ │ │ │ │ │ .IP "\-c \-\-cropped-base=crop" │ │ │ │ Base name for the cropped image files, the file type and numbering will be based on the input image file type and numbering. │ │ │ │ │ │ │ │ .IP "\-e \-\-enlarge=5" │ │ │ │ Enlarge the area around the obtained sbounding box by this number of pixels in each direction │ │ ├── ./usr/share/man/man1/mia-2dsegshift.1.gz │ │ │ ├── mia-2dsegshift.1 │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dsegshift \-i \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dsegshift │ │ │ │ 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. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ +.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ input segmentation set │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ input segmentation set │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-g \-\-image-file=crop" │ │ │ │ output image filename base │ │ │ │ │ │ │ │ .IP "\-S \-\-shift=[0,0]" │ │ │ │ shift of segmentation │ │ ├── ./usr/share/man/man1/mia-2dsegshiftperslice.1.gz │ │ │ ├── mia-2dsegshiftperslice.1 │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dsegshiftperslice \-i \-o \-S [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dsegshiftperslice │ │ │ │ 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. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ +.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ input segmentation set │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(output, required); string" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); string" │ │ │ │ output segmentation set │ │ │ │ │ │ │ │ .IP "\-g \-\-image-file=crop" │ │ │ │ output image filename base │ │ │ │ │ │ │ │ .IP "\-S \-\-shift=(required); string" │ │ │ │ shift of segmentation \- base name │ │ ├── ./usr/share/man/man1/mia-2dseries-mincorr.1.gz │ │ │ ├── mia-2dseries-mincorr.1 │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dseries\-mincorr \-i \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dseries\-mincorr │ │ │ │ Given a set of images of temporal sucession, this program evaluates the minimal correlation of the time-intensity curve between neighboring pixels. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-set=(required, input); string" │ │ │ │ +.IP "\-i \-\-in-set=(input, required); string" │ │ │ │ input segmentation set │ │ │ │ │ │ │ │ .IP "\-o \-\-out-set=(required, output); io" │ │ │ │ output image of minimal correlation │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-k \-\-skip=2" │ │ │ │ skip images at beginning of series │ │ ├── ./usr/share/man/man1/mia-2dseries2dordermedian.1.gz │ │ │ ├── mia-2dseries2dordermedian.1 │ │ │ │ @@ -8,15 +8,15 @@ │ │ │ │ .B mia\-2dseries2dordermedian │ │ │ │ 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). │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-in-file=(input, required); string" │ │ │ │ input segmentation set │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ output image name │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-k \-\-skip=0" │ │ │ │ Skip files at the beginning │ │ │ │ │ │ │ │ .IP "\-e \-\-enlarge-boundary=5" │ │ │ │ Enlarge cropbox by number of pixels │ │ │ │ @@ -842,15 +842,15 @@ │ │ │ │ Intensity thresholding parameter: Pixels with intensities below this threshold will be set to zero, and also not used when evaluating mean and variation. │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ varfile │ │ │ │ -=(required, output, io) │ │ │ │ +=(output, required, io) │ │ │ │ .RS 2 │ │ │ │ name of the output file to save the variation image too.. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ @@ -878,15 +878,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B 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: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ madfile │ │ │ │ -=(required, output, io) │ │ │ │ +=(output, required, io) │ │ │ │ .RS 2 │ │ │ │ name of the output file to save the median absolute deviation image too.. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ @@ -1197,15 +1197,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B tee │ │ │ │ Save the input image to a file and also pass it through to the next filter, supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ file │ │ │ │ -=(required, output, io) │ │ │ │ +=(output, required, io) │ │ │ │ .RS 2 │ │ │ │ name of the output file to save the image too.. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ ├── ./usr/share/man/man1/mia-2dseries2sets.1.gz │ │ │ ├── mia-2dseries2sets.1 │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dseries2sets \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dseries2sets │ │ │ │ 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. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-o \-\-out-directory=(required, output); string" │ │ │ │ +.IP "\-o \-\-out-directory=(output, required); string" │ │ │ │ output directory (needs to exist and be writable) │ │ │ │ │ │ │ │ .IP " \-\-no-copy" │ │ │ │ don't copy image files to output directory │ │ │ │ │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ ├── ./usr/share/man/man1/mia-2dseriescorr.1.gz │ │ │ ├── mia-2dseriescorr.1 │ │ │ │ @@ -8,15 +8,15 @@ │ │ │ │ .B mia\-2dseriescorr │ │ │ │ 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. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-in-base=(input, required); io" │ │ │ │ input file name base │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-o \-\-outname=(required, output); io" │ │ │ │ +.IP "\-o \-\-outname=(output, required); io" │ │ │ │ output file name to save the avarage per\-pixel correlation │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-z \-\-horizontal=(output); io" │ │ │ │ horiZontal correlation output file name │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-t \-\-vertical=(output); io" │ │ │ │ verTical correlation output file name │ │ ├── ./usr/share/man/man1/mia-2dseriesgradMAD.1.gz │ │ │ ├── mia-2dseriesgradMAD.1 │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dseriesgradMAD \-i \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dseriesgradMAD │ │ │ │ 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). │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ +.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ input segmentation set │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ output file name │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-k \-\-skip=0" │ │ │ │ Skip files at the beginning │ │ │ │ │ │ │ │ .IP "\-e \-\-enlarge-boundary=5" │ │ │ │ Enlarge cropbox by number of pixels │ │ │ │ @@ -355,15 +355,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B 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: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ image │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ second image that is needed in the combiner. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ @@ -699,15 +699,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B labelmap │ │ │ │ Image filter to remap label id's. Only applicable to images with integer valued intensities/labels., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ map │ │ │ │ -=(input, required, string) │ │ │ │ +=(required, input, string) │ │ │ │ .RS 2 │ │ │ │ Label mapping file. │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ .B labelscale │ │ │ │ @@ -725,15 +725,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B load │ │ │ │ Load the input image from a file and use it to replace the current image in the pipeline., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ file │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ name of the input file to load from.. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ @@ -764,15 +764,15 @@ │ │ │ │ .RE │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ input │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ second input image file name. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ @@ -787,25 +787,25 @@ │ │ │ │ .TP 10 │ │ │ │ .B maxflow │ │ │ │ This filter implements the uses the max-flow min-cut algorithmfor image segmentation, supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ sink-flow │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ Image of float type to define the per\-pixel flow to the sink. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ source-flow │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ Image of float type to define the per\-pixel flow to the source. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ @@ -833,15 +833,15 @@ │ │ │ │ Intensity thresholding parameter: Pixels with intensities below this threshold will be set to zero, and also not used when evaluating mean and variation. │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ varfile │ │ │ │ -=(required, output, io) │ │ │ │ +=(output, required, io) │ │ │ │ .RS 2 │ │ │ │ name of the output file to save the variation image too.. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ @@ -869,15 +869,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B 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: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ madfile │ │ │ │ -=(required, output, io) │ │ │ │ +=(output, required, io) │ │ │ │ .RS 2 │ │ │ │ name of the output file to save the median absolute deviation image too.. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ @@ -994,15 +994,15 @@ │ │ │ │ For supported plug-ins see PLUGINS:2dimage/shape │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ seed │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ seed image (bit valued). │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ @@ -1175,28 +1175,28 @@ │ │ │ │ For supported plug-ins see PLUGINS:2dimage/shape │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ seed │ │ │ │ -=(input, required, string) │ │ │ │ +=(required, input, string) │ │ │ │ .RS 2 │ │ │ │ seed input image containing the lables for the initial regions. │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ .B tee │ │ │ │ Save the input image to a file and also pass it through to the next filter, supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ file │ │ │ │ -=(required, output, io) │ │ │ │ +=(output, required, io) │ │ │ │ .RS 2 │ │ │ │ name of the output file to save the image too.. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ @@ -1260,15 +1260,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B transform │ │ │ │ Transform the input image with the given transformation., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ file │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ Name of the file containing the transformation.. │ │ │ │ For supported file types see PLUGINS:2dtransform/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ ├── ./usr/share/man/man1/mia-2dseriessmoothgradMAD.1.gz │ │ │ ├── mia-2dseriessmoothgradMAD.1 │ │ │ │ @@ -8,15 +8,15 @@ │ │ │ │ .B mia\-2dseriessmoothgradMAD │ │ │ │ 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) │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-in-file=(input, required); string" │ │ │ │ input segmentation set │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ output file name │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-k \-\-skip=0" │ │ │ │ Skip files at the beginning │ │ │ │ │ │ │ │ .IP "\-e \-\-enlarge-boundary=5" │ │ │ │ Enlarge cropbox by number of pixels │ │ │ │ @@ -836,15 +836,15 @@ │ │ │ │ Intensity thresholding parameter: Pixels with intensities below this threshold will be set to zero, and also not used when evaluating mean and variation. │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ varfile │ │ │ │ -=(required, output, io) │ │ │ │ +=(output, required, io) │ │ │ │ .RS 2 │ │ │ │ name of the output file to save the variation image too.. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ @@ -872,15 +872,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B 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: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ madfile │ │ │ │ -=(required, output, io) │ │ │ │ +=(output, required, io) │ │ │ │ .RS 2 │ │ │ │ name of the output file to save the median absolute deviation image too.. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ @@ -1191,15 +1191,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B tee │ │ │ │ Save the input image to a file and also pass it through to the next filter, supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ file │ │ │ │ -=(required, output, io) │ │ │ │ +=(output, required, io) │ │ │ │ .RS 2 │ │ │ │ name of the output file to save the image too.. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ ├── ./usr/share/man/man1/mia-2dseriestovolume.1.gz │ │ │ ├── mia-2dseriestovolume.1 │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dseriestovolume \-i \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dseriestovolume │ │ │ │ Obtaines a 3D volume image by combining the images of the segmentation set. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ input segmentation set │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ output 3D image │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ .IP "\-k \-\-skip=0" │ │ │ │ number of frames to skip at the beginning of the series. │ │ │ │ │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ ├── ./usr/share/man/man1/mia-2dstack-cmeans-presegment.1.gz │ │ │ ├── mia-2dstack-cmeans-presegment.1 │ │ │ │ @@ -6,24 +6,24 @@ │ │ │ │ .B mia\-2dstack\-cmeans\-presegment \-i \-o \-L