--- /srv/rebuilderd/tmp/rebuilderdT9QRPY/inputs/mia-tools_2.4.7-16_ppc64el.deb +++ /srv/rebuilderd/tmp/rebuilderdT9QRPY/out/mia-tools_2.4.7-16_ppc64el.deb ├── file list │ @@ -1,3 +1,3 @@ │ -rw-r--r-- 0 0 0 4 2025-10-24 23:01:09.000000 debian-binary │ -rw-r--r-- 0 0 0 7576 2025-10-24 23:01:09.000000 control.tar.xz │ --rw-r--r-- 0 0 0 1919704 2025-10-24 23:01:09.000000 data.tar.xz │ +-rw-r--r-- 0 0 0 1920180 2025-10-24 23:01:09.000000 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 2025-10-24 23:01:09.000000 ./usr/share/doc/mia-tools/copyright │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-10-24 23:01:09.000000 ./usr/share/lintian/ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-10-24 23:01:09.000000 ./usr/share/lintian/overrides/ │ │ │ -rw-r--r-- 0 root (0) root (0) 186 2025-10-24 23:01:09.000000 ./usr/share/lintian/overrides/mia-tools │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-10-24 23:01:09.000000 ./usr/share/man/ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-10-24 23:01:09.000000 ./usr/share/man/man1/ │ │ │ --rw-r--r-- 0 root (0) root (0) 1472 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2davgmasked.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1565 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dbinarycombine.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1474 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2davgmasked.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1571 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dbinarycombine.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 2633 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dcost.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1746 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2ddeform.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1690 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2ddistance.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1691 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2ddistance.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1867 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2deval-transformquantity.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 3500 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dfluid-syn-registration.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1915 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dfluid.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1548 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dforce.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1543 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dforce.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1806 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dfuzzysegment.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1592 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dgrayimage-combine-to-rgb.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1590 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dgrayimage-combine-to-rgb.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 3457 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dgroundtruthreg.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1469 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dimagecombine-dice.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1470 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dimagecombine-dice.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1620 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dimagecombiner.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1772 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dimagecreator.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 6176 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dimagefilter.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 6372 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dimagefilterstack.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1442 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dimagefullstats.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 5276 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dimageregistration.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1495 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dimageselect.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1490 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dimageselect.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1428 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dimageseries-maximum-intensity-projection.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1949 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dimagestack-cmeans.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1622 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dimagestats.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1669 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dlerp.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 3675 2025-10-24 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│ │ │ --rw-r--r-- 0 root (0) root (0) 1817 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dmyocard-icaseries.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 2194 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dmyocard-ica.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1815 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dmyocard-icaseries.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1731 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dmyocard-segment.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 6381 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dmyoica-full.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 5456 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dmyoica-nonrigid-parallel.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 5394 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dmyoica-nonrigid.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 3710 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dmyoica-nonrigid2.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 6761 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2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dseries-mincorr.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1516 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dseries-sectionmask.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 976 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dseries-segdistance.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 6401 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dseries2dordermedian.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1132 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dsegshiftperslice.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1574 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dseries-mincorr.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1511 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dseries-sectionmask.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 977 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dseries-segdistance.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 6399 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dseries2dordermedian.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1725 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dseries2sets.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1713 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dseriescorr.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 6297 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dseriesgradMAD.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1725 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dseriesgradvariation.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 993 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dserieshausdorff.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 6341 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dseriessmoothgradMAD.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1574 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dseriestovolume.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1728 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dseriesgradvariation.1.gz │ │ │ 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./usr/share/man/man1/mia-2dto3dimageb.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1369 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dtrackpixelmovement.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1669 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dtransform.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1117 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dtransformation-to-strain.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1630 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dbinarycombine.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1366 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dtrackpixelmovement.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1674 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dtransform.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1122 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dtransformation-to-strain.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1628 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dbinarycombine.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1879 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dbrainextractT1.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1740 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dcombine-imageseries.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1655 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dcombine-mr-segmentations.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 3428 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dcost-translatedgrad.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 6734 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dcost.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1646 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dcrispsegment.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1864 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3ddeform.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 2011 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3ddistance-stats.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1739 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dcombine-imageseries.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1651 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dcombine-mr-segmentations.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 3432 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dcost-translatedgrad.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 6733 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dcost.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1645 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dcrispsegment.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1866 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3ddeform.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 2012 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3ddistance-stats.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1141 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3ddistance.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1878 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3deval-transformquantity.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1670 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dfield2norm.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1668 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dfield2norm.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 3573 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dfluid-syn-registration.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 2319 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dfluid.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 2365 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dforce.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1707 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dfuzzysegment.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1468 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dgetsize.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 2199 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dgetslice.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1469 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dgetsize.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 2203 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dgetslice.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1968 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dimageaddattributes.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1658 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dimagecombine.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1907 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dimagecreator.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 5694 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dimagefilter.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 5897 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dimagefilterstack.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1544 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dimageselect.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 5893 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dimagefilterstack.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1543 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dimageselect.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1934 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dimagestatistics-in-mask.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1544 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dimagestats.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1263 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3disosurface-from-stack.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 2266 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3disosurface-from-volume.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1545 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dimagestats.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1264 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3disosurface-from-stack.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 2267 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3disosurface-from-volume.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1140 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dlandmarks-distances.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1295 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dlandmarks-transform.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1296 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dlandmarks-transform.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1722 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dlerp.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 7892 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dmany2one-nonrigid.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1871 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dmaskseeded.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 2559 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dmotioncompica-nonrigid.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 7894 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dmany2one-nonrigid.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1876 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dmaskseeded.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 2563 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dmotioncompica-nonrigid.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 9542 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dnonrigidreg-alt.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 9403 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dnonrigidreg.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 10017 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dprealign-nonrigid.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 5801 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dpropose-boundingbox.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 9401 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dnonrigidreg.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 10023 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dprealign-nonrigid.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 5802 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dpropose-boundingbox.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 5112 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3drigidreg.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1936 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dsegment-ahmed.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 2572 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dsegment-local-cmeans.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1930 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dsegment-ahmed.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 2567 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dsegment-local-cmeans.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 9436 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dserial-nonrigid.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1586 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dseries-track-intensity.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1369 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dtrackpixelmovement.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1585 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dseries-track-intensity.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1375 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dtrackpixelmovement.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1710 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dtransform.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1313 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dtransform2vf.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1268 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dvectorfieldcreate.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1660 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dvf2transform.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1317 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dtransform2vf.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1267 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dvectorfieldcreate.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1656 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dvf2transform.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1267 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dvfcompare.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1121 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-cmeans.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 883 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-filenumberpattern.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 986 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-labelsort.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 6456 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-mesh-deformable-model.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 2140 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-mesh-to-maskimage.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 991 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-labelsort.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 6462 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-mesh-deformable-model.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 2142 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-mesh-to-maskimage.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1954 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-meshdistance-to-stackmask.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 2435 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-meshfilter.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1660 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-multihist.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 900 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-myowavelettest.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 2433 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-meshfilter.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1656 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-multihist.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 901 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-myowavelettest.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 850 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-plugin-help.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1740 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-raw2image.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1736 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-raw2image.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1806 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-raw2volume.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1092 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-wavelettrans.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1086 2025-10-24 23:01:09.000000 ./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 │ │ │ │ @@ -11,15 +11,15 @@ │ │ │ │ .RS │ │ │ │ .IP "\-1 \-\-file1=(input, required); io" │ │ │ │ input mask image 1 │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-2 \-\-file2=(input, required); io" │ │ │ │ input mask image 2 │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); 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-2ddistance.1.gz │ │ │ ├── mia-2ddistance.1 │ │ │ │ @@ -5,21 +5,21 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2ddistance \-i \-d \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2ddistance │ │ │ │ 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. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ +.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ input image │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-d \-\-distance-file=(input, required); 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-2deval-transformquantity.1.gz │ │ │ ├── mia-2deval-transformquantity.1 │ │ │ │ @@ -24,21 +24,21 @@ │ │ │ │ } │ │ │ │ │ │ │ │ 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. │ │ │ │ .SH OPTIONS │ │ │ │ .SS │ │ │ │ File-IO │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ +.IP "\-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. │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(required, output); string" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); string" │ │ │ │ output strains file, for a format description see above. │ │ │ │ │ │ │ │ -.IP "\-t \-\-transformation=(required, input); io" │ │ │ │ +.IP "\-t \-\-transformation=(input, required); io" │ │ │ │ transformation of which the quantity will be evaluated. │ │ │ │ For supported file types see PLUGINS:2dtransform/io │ │ │ │ .RE │ │ │ │ .SS │ │ │ │ Parameters │ │ │ │ .RS │ │ │ │ .IP "\-q \-\-quantity=strain" │ │ ├── ./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-2dgrayimage-combine-to-rgb.1.gz │ │ │ ├── mia-2dgrayimage-combine-to-rgb.1 │ │ │ │ @@ -14,15 +14,15 @@ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-g \-\-green=(input); io" │ │ │ │ input image for green channel │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-r \-\-red=(input); io" │ │ │ │ input image for red channel │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ combined 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-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-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-2dimageselect.1.gz │ │ │ ├── mia-2dimageselect.1 │ │ │ │ @@ -8,15 +8,15 @@ │ │ │ │ .B mia\-2dimageselect │ │ │ │ This program is used to select one 2D images from a multi-image file. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-in-file=(input, required); io" │ │ │ │ input images │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ output image │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-n \-\-number=0" │ │ │ │ image number to be selected │ │ │ │ │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ ├── ./usr/share/man/man1/mia-2dlerp.1.gz │ │ │ ├── mia-2dlerp.1 │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ .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" │ │ │ │ output vector field │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-p \-\-positions=(required); vfloat" │ │ │ │ image series positions (first, target, second) │ │ ├── ./usr/share/man/man1/mia-2dmany2one-nonrigid.1.gz │ │ │ ├── mia-2dmany2one-nonrigid.1 │ │ │ │ @@ -7,18 +7,18 @@ │ │ │ │ .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=(required, input); string" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ input perfusion data set │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(output, required); string" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); string" │ │ │ │ file name for registered images, numbering and pattern are deducted from the input data │ │ │ │ │ │ │ │ .RE │ │ │ │ .SS │ │ │ │ Registration │ │ │ │ .RS │ │ │ │ .IP "\-O \-\-optimizer=gsl:opt=gd,step=0.1" │ │ ├── ./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=(required, output); io" │ │ │ │ +.IP "\-o \-\-out-transform=(output, required); 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-2dmyocard-ica.1.gz │ │ │ ├── mia-2dmyocard-ica.1 │ │ │ │ @@ -6,15 +6,15 @@ │ │ │ │ .B mia\-2dmyocard\-ica \-i [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dmyocard\-ica │ │ │ │ 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. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-base=(required, input); io" │ │ │ │ +.IP "\-i \-\-in-base=(input, required); io" │ │ │ │ input file name ofolloing pattern nameXXXX.ext X=numbers │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP " \-\-coefs=" │ │ │ │ output mixing coefficients to this file │ │ │ │ │ │ │ │ .IP "\-o \-\-out-base=(output); string" │ │ │ │ output file name base │ │ ├── ./usr/share/man/man1/mia-2dmyocard-icaseries.1.gz │ │ │ ├── mia-2dmyocard-icaseries.1 │ │ │ │ @@ -6,15 +6,15 @@ │ │ │ │ .B mia\-2dmyocard\-icaseries \-i [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dmyocard\-icaseries │ │ │ │ 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. │ │ │ │ .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 "\-r \-\-references=(output); string" │ │ │ │ File name base for the reference images. Image type and numbering scheme are taken from the input images. │ │ │ │ │ │ │ │ .IP "\-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 │ │ ├── ./usr/share/man/man1/mia-2dmyoica-full.1.gz │ │ │ ├── mia-2dmyoica-full.1 │ │ │ │ @@ -14,15 +14,15 @@ │ │ │ │ .UE │ │ │ │ .RE │ │ │ │ │ │ │ │ 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. │ │ │ │ .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=(required, output); string" │ │ │ │ output perfusion data set │ │ │ │ │ │ │ │ .IP "\-r \-\-registered=" │ │ │ │ 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-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 │ │ │ │ @@ -16,15 +16,15 @@ │ │ │ │ │ │ │ │ .SH OPTIONS │ │ │ │ .SS File-IO │ │ │ │ .RS │ │ │ │ .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-2dmyoica-nonrigid2.1.gz │ │ │ ├── mia-2dmyoica-nonrigid2.1 │ │ │ │ @@ -8,15 +8,15 @@ │ │ │ │ .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=(required, input); string" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); 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-2dmyoicapgt.1.gz │ │ │ ├── mia-2dmyoicapgt.1 │ │ │ │ @@ -43,18 +43,18 @@ │ │ │ │ │ │ │ │ .IP "\-T \-\-rho-thresh=0.85" │ │ │ │ correlation threshold for neighborhood analysis │ │ │ │ │ │ │ │ .RE │ │ │ │ .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=" │ │ │ │ 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. │ │ │ │ │ │ │ │ .IP " \-\-save-cropped=(output); string" │ │ │ │ save cropped set to this file, the image files will use the stem of the name as file name base │ │ ├── ./usr/share/man/man1/mia-2dmyomilles.1.gz │ │ │ ├── mia-2dmyomilles.1 │ │ │ │ @@ -15,15 +15,15 @@ │ │ │ │ .RE │ │ │ │ │ │ │ │ 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. │ │ │ │ │ │ │ │ .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=" │ │ │ │ file name base for registered files │ │ ├── ./usr/share/man/man1/mia-2dmyopgt-nonrigid.1.gz │ │ │ ├── mia-2dmyopgt-nonrigid.1 │ │ │ │ @@ -16,15 +16,15 @@ │ │ │ │ │ │ │ │ . │ │ │ │ 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=(required, output); 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 │ │ ├── ./usr/share/man/man1/mia-2dmyoserial-nonrigid.1.gz │ │ │ ├── mia-2dmyoserial-nonrigid.1 │ │ │ │ @@ -17,15 +17,15 @@ │ │ │ │ .SH OPTIONS │ │ │ │ .SS │ │ │ │ File-IO │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-in-file=(input, required); 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 fiels │ │ │ │ │ │ │ │ .RE │ │ │ │ .SS │ │ ├── ./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=(required, input); string" │ │ │ │ +.IP "\-i \-\-input=(input, required); 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 │ │ │ │ @@ -10,15 +10,15 @@ │ │ │ │ .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 " \-\-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 │ │ │ │ @@ -13,15 +13,15 @@ │ │ │ │ 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" │ │ │ │ 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 │ │ ├── ./usr/share/man/man1/mia-2dsegment-local-cmeans.1.gz │ │ │ ├── mia-2dsegment-local-cmeans.1 │ │ │ │ @@ -13,15 +13,15 @@ │ │ │ │ Dunmore CJ, Wollny G, Skinner MM. (2018) MIA-Clustering: a novel method for segmentation of paleontological material. PeerJ 6:e4374. │ │ │ │ .UE │ │ │ │ .RE │ │ │ │ │ │ │ │ .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); io" │ │ │ │ class label image based on merging local labels │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-G \-\-out-global-crisp=(output); io" │ │ │ │ class label image based on global segmentation │ │ ├── ./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=(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=(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=(required, output); string" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); 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-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=(required, input); string" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ input segmentation set │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(required, output); string" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); 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 succession, 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=(output, required); 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-2dseries-sectionmask.1.gz │ │ │ ├── mia-2dseries-sectionmask.1 │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dseries\-sectionmask \-i \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dseries\-sectionmask │ │ │ │ Evaluate the masks for the sections of a segmented frame. │ │ │ │ .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" │ │ │ │ output image containing the mask │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-f \-\-frame=0" │ │ │ │ Frame number for which to extract the mask │ │ ├── ./usr/share/man/man1/mia-2dseries-segdistance.1.gz │ │ │ ├── mia-2dseries-segdistance.1 │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dseries\-segdistance \-i [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dseries\-segdistance │ │ │ │ Get the mean distance of a segmentation boundary to the reference boundary. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ +.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ input segmentation set │ │ │ │ │ │ │ │ .IP "\-r \-\-reference=20" │ │ │ │ reference frame │ │ │ │ │ │ │ │ .IP "\-k \-\-skip=0" │ │ │ │ skip images at the beginning │ │ ├── ./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=(required, input); string" │ │ │ │ input segmentation set │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); 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 │ │ │ │ -=(output, required, io) │ │ │ │ +=(required, output, 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 │ │ │ │ -=(output, required, io) │ │ │ │ +=(required, output, 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 │ │ │ │ -=(output, required, io) │ │ │ │ +=(required, output, 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-2dseriescorr.1.gz │ │ │ ├── mia-2dseriescorr.1 │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dseriescorr \-i \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dseriescorr │ │ │ │ Given a set of images of temporal succession, 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" │ │ │ │ +.IP "\-i \-\-in-base=(required, input); io" │ │ │ │ input file name base │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-o \-\-outname=(output, required); io" │ │ │ │ +.IP "\-o \-\-outname=(required, output); 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-2dseriesgradvariation.1.gz │ │ │ ├── mia-2dseriesgradvariation.1 │ │ │ │ @@ -8,15 +8,15 @@ │ │ │ │ .B mia\-2dseriesgradvariation │ │ │ │ Given a set of images of temporal succession, 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. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ .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 │ │ ├── ./usr/share/man/man1/mia-2dserieshausdorff.1.gz │ │ │ ├── mia-2dserieshausdorff.1 │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dserieshausdorff \-i \-r [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dserieshausdorff │ │ │ │ Get the per-slice Hausdorff distance of a segmentation with respect to a given reference segmentation set. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ input segmentation set │ │ │ │ │ │ │ │ -.IP "\-r \-\-ref-file=(required, input); string" │ │ │ │ +.IP "\-r \-\-ref-file=(input, required); string" │ │ │ │ reference segmentation set │ │ │ │ │ │ │ │ .IP "\-k \-\-skip=0" │ │ │ │ skip images at the beginning │ │ │ │ │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ ├── ./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 succession, 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=(output, required); io" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); 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 │ │ │ │ -=(output, required, io) │ │ │ │ +=(required, output, 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 │ │ │ │ -=(output, required, io) │ │ │ │ +=(required, output, 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 │ │ │ │ -=(output, required, io) │ │ │ │ +=(required, output, 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 │ │ │ │ @@ -8,15 +8,15 @@ │ │ │ │ .B mia\-2dseriestovolume │ │ │ │ Obtaines a 3D volume image by combining the images of the segmentation set. │ │ │ │ .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 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-2dstackfilter.1.gz │ │ │ ├── mia-2dstackfilter.1 │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dstackfilter \-i \-o \-t [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dstackfilter │ │ │ │ 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. │ │ │ │ .SH OPTIONS │ │ │ │ .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" │ │ │ │ +.IP "\-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 PLUGINS:2dimage/io │ │ │ │ .IP "\-t \-\-type=(required); set" │ │ │ │ output file type │ │ │ │ │ │ │ │ .RS 10 │ │ │ │ .I │ │ │ │ @@ -378,15 +378,15 @@ │ │ │ │ .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 │ │ │ │ @@ -722,15 +722,15 @@ │ │ │ │ .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 │ │ │ │ @@ -748,15 +748,15 @@ │ │ │ │ .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 │ │ │ │ @@ -787,15 +787,15 @@ │ │ │ │ .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 │ │ │ │ @@ -810,25 +810,25 @@ │ │ │ │ .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 │ │ │ │ @@ -856,15 +856,15 @@ │ │ │ │ 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 │ │ │ │ -=(output, required, io) │ │ │ │ +=(required, output, 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 │ │ │ │ @@ -892,15 +892,15 @@ │ │ │ │ .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 │ │ │ │ -=(output, required, io) │ │ │ │ +=(required, output, 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 │ │ │ │ @@ -1017,15 +1017,15 @@ │ │ │ │ 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 │ │ │ │ @@ -1198,28 +1198,28 @@ │ │ │ │ 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 labels 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 │ │ │ │ -=(output, required, io) │ │ │ │ +=(required, output, 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 │ │ │ │ @@ -1283,15 +1283,15 @@ │ │ │ │ .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 │ │ │ │ @@ -1625,15 +1625,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B label │ │ │ │ Stack Label filter, supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ map │ │ │ │ -=(input, required, string) │ │ │ │ +=(required, input, string) │ │ │ │ .RS 2 │ │ │ │ Mapfile to save label numbers that are joined. │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ @@ -1715,15 +1715,15 @@ │ │ │ │ low threshold for acceptance probability. │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ map │ │ │ │ -=(input, required, string) │ │ │ │ +=(required, input, string) │ │ │ │ .RS 2 │ │ │ │ seed class map. │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ ├── ./usr/share/man/man1/mia-2dto3dimage.1.gz │ │ │ ├── mia-2dto3dimage.1 │ │ │ │ @@ -8,15 +8,15 @@ │ │ │ │ .B mia\-2dto3dimage │ │ │ │ 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. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-in-file=(required, input); io" │ │ │ │ input image(s) to be combined │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ output file name │ │ │ │ For supported file types see PLUGINS:3dimage/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-2dtrackpixelmovement.1.gz │ │ │ ├── mia-2dtrackpixelmovement.1 │ │ │ │ @@ -10,21 +10,21 @@ │ │ │ │ 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. │ │ │ │ .SH OPTIONS │ │ │ │ .SS │ │ │ │ File-IO │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ input point set │ │ │ │ │ │ │ │ .IP "\-o \-\-out-file=(output, required); string" │ │ │ │ output point set │ │ │ │ │ │ │ │ -.IP "\-t \-\-transformation=(required, input); io" │ │ │ │ +.IP "\-t \-\-transformation=(input, required); io" │ │ │ │ transformation describing the monitored change │ │ │ │ For supported file types see PLUGINS:2dtransform/io │ │ │ │ .RE │ │ │ │ .SS │ │ │ │ Parameters │ │ │ │ .RS │ │ │ │ .IP "\-T \-\-time-step=1" │ │ ├── ./usr/share/man/man1/mia-2dtransform.1.gz │ │ │ ├── mia-2dtransform.1 │ │ │ │ @@ -5,21 +5,21 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dtransform \-i \-o \-t [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dtransform │ │ │ │ This program is used to deform a 2D image using a given transformation. │ │ │ │ .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 │ │ │ │ .IP "\-o \-\-out-file=(required, output); io" │ │ │ │ output image │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-t \-\-transformation=(required, input); io" │ │ │ │ +.IP "\-t \-\-transformation=(input, required); io" │ │ │ │ transformation file name │ │ │ │ For supported file types see PLUGINS:2dtransform/io │ │ │ │ .IP "\-p \-\-interpolator=" │ │ │ │ override the interpolator provided by the transformation │ │ │ │ │ │ │ │ .IP "\-b \-\-boundary=mirror" │ │ │ │ override the boundary conditions provided by the transformation. This is only used if the interpolator is overridden. │ │ ├── ./usr/share/man/man1/mia-2dtransformation-to-strain.1.gz │ │ │ ├── mia-2dtransformation-to-strain.1 │ │ │ │ @@ -8,15 +8,15 @@ │ │ │ │ .B mia\-2dtransformation\-to\-strain │ │ │ │ Evaluate the Green strain tensor corresponding to a given 2D transformation for each grid point. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-in-file=(input, required); io" │ │ │ │ input transformation │ │ │ │ For supported file types see PLUGINS:2dtransform/io │ │ │ │ -.IP "\-o \-\-out-file=(output, required); string" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); string" │ │ │ │ output Green's strain tensor │ │ │ │ │ │ │ │ .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-3dbinarycombine.1.gz │ │ │ ├── mia-3dbinarycombine.1 │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-3dbinarycombine \-1 \-2 \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-3dbinarycombine │ │ │ │ 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:3dimage/io │ │ │ │ -.IP "\-2 \-\-file2=(required, input); io" │ │ │ │ +.IP "\-2 \-\-file2=(input, required); io" │ │ │ │ input mask image 2 │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ .IP "\-p \-\-operation=nor" │ │ │ │ Operation to be applied │ │ │ │ │ │ │ │ .RS 10 │ │ │ │ .I │ │ │ │ @@ -44,15 +44,15 @@ │ │ │ │ \(hy logocal xor │ │ │ │ .RE │ │ │ │ .RS 10 │ │ │ │ .I │ │ │ │ nxor │ │ │ │ \(hy logocal nxor │ │ │ │ .RE │ │ │ │ -.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ output mask image │ │ │ │ For supported file types see PLUGINS:3dimage/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-3dbrainextractT1.1.gz │ │ │ ├── mia-3dbrainextractT1.1 │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-3dbrainextractT1 \-i \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-3dbrainextractT1 │ │ │ │ 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. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ input image(s) to be segmented │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ -.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ brain mask │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ .IP "\-n \-\-no-of-classes=3" │ │ │ │ number of classes │ │ │ │ │ │ │ │ .IP "\-w \-\-wm-class=2" │ │ │ │ index of white matter │ │ ├── ./usr/share/man/man1/mia-3dcombine-imageseries.1.gz │ │ │ ├── mia-3dcombine-imageseries.1 │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-3dcombine\-imageseries \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-3dcombine\-imageseries │ │ │ │ This programs takes various input images of the same dimensions and creates a combined output images that uses the define operation for the combination. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ output file that contains the combined image. │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ .IP "\-p \-\-operation=mean" │ │ │ │ Operation to be applied when combining the images │ │ │ │ │ │ │ │ .RS 10 │ │ │ │ .I │ │ ├── ./usr/share/man/man1/mia-3dcombine-mr-segmentations.1.gz │ │ │ ├── mia-3dcombine-mr-segmentations.1 │ │ │ │ @@ -8,15 +8,15 @@ │ │ │ │ .B mia\-3dcombine\-mr\-segmentations │ │ │ │ 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. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ .IP "\-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 PLUGINS:3dimage/io │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ output image that contains the labeling. │ │ │ │ For supported file types see PLUGINS:3dimage/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-3dcost-translatedgrad.1.gz │ │ │ ├── mia-3dcost-translatedgrad.1 │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-3dcost\-translatedgrad \-i \-r \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-3dcost\-translatedgrad │ │ │ │ Evaluate the cost gradient between two images and evaluate the transformation related gradient for it based on the given transformation model. │ │ │ │ .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:3dimage/io │ │ │ │ -.IP "\-r \-\-ref-file=(required, input); io" │ │ │ │ +.IP "\-r \-\-ref-file=(input, required); io" │ │ │ │ reference image │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ .IP "\-o \-\-out-file=(required, output); io" │ │ │ │ output vector field │ │ │ │ For supported file types see PLUGINS:3dtransform/io │ │ │ │ .IP "\-g \-\-gradimg-file=(output); io" │ │ │ │ norm image of the spline transformed gradient │ │ ├── ./usr/share/man/man1/mia-3dcost.1.gz │ │ │ ├── mia-3dcost.1 │ │ │ │ @@ -403,15 +403,15 @@ │ │ │ │ .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:3dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ @@ -717,15 +717,15 @@ │ │ │ │ lower threshold for mask growing. │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ ref │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ reference image for mask region growing. │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ @@ -798,15 +798,15 @@ │ │ │ │ .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 │ │ │ │ @@ -824,15 +824,15 @@ │ │ │ │ .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:3dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ @@ -851,15 +851,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B 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: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ input │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ second input image file name. │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ @@ -1241,15 +1241,15 @@ │ │ │ │ For supported plug-ins see PLUGINS:3dimage/shape │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ seed │ │ │ │ -=(input, required, string) │ │ │ │ +=(required, input, string) │ │ │ │ .RS 2 │ │ │ │ seed input image containing the labels for the initial regions. │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ .B tee │ │ │ │ @@ -1275,15 +1275,15 @@ │ │ │ │ .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:3dtransform/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ ├── ./usr/share/man/man1/mia-3dcrispsegment.1.gz │ │ │ ├── mia-3dcrispsegment.1 │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-3dcrispsegment \-i \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-3dcrispsegment │ │ │ │ This program creates a label image from a fuzzy segmentation. or each pixel the label is set to the class with the highest probability plus a given offset │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ input class file, should contain multiple images with tissue class probabilities │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ -.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ output class label image │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ .IP "\-l \-\-label-offset=1" │ │ │ │ label offset │ │ │ │ │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ ├── ./usr/share/man/man1/mia-3ddeform.1.gz │ │ │ ├── mia-3ddeform.1 │ │ │ │ @@ -5,21 +5,21 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-3ddeform \-i \-o \-t [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-3ddeform │ │ │ │ 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) │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-image=(input, required); io" │ │ │ │ +.IP "\-i \-\-in-image=(required, input); io" │ │ │ │ input image │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ -.IP "\-o \-\-out-image=(output, required); io" │ │ │ │ +.IP "\-o \-\-out-image=(required, output); io" │ │ │ │ transformed image │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ -.IP "\-t \-\-transformation=(input, required); io" │ │ │ │ +.IP "\-t \-\-transformation=(required, input); io" │ │ │ │ transformation vector field │ │ │ │ For supported file types see PLUGINS:3dvf/io │ │ │ │ .IP "\-p \-\-interpolator=bspline:d=3" │ │ │ │ image interpolator kernel │ │ │ │ For supported plugins see PLUGINS:1d/splinekernel │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ ├── ./usr/share/man/man1/mia-3ddistance-stats.1.gz │ │ │ ├── mia-3ddistance-stats.1 │ │ │ │ @@ -24,24 +24,24 @@ │ │ │ │ cat(result) │ │ │ │ } │ │ │ │ │ │ │ │ │ │ │ │ .SH OPTIONS │ │ │ │ .SS File-IO │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-labels=(required, input); io" │ │ │ │ +.IP "\-i \-\-in-labels=(input, required); io" │ │ │ │ input label image │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ -.IP "\-r \-\-ref-labels=(required, input); io" │ │ │ │ +.IP "\-r \-\-ref-labels=(input, required); io" │ │ │ │ reference label image │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ .IP "\-l \-\-label-map=(input); string" │ │ │ │ optional mapping of label numbers │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(required, output); string" │ │ │ │ +.IP "\-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. │ │ │ │ │ │ │ │ .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-3deval-transformquantity.1.gz │ │ │ ├── mia-3deval-transformquantity.1 │ │ │ │ @@ -27,18 +27,18 @@ │ │ │ │ .SH OPTIONS │ │ │ │ .SS │ │ │ │ File-IO │ │ │ │ .RS │ │ │ │ .IP "\-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. │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(output, required); string" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); string" │ │ │ │ output strains file, for a format description see above. │ │ │ │ │ │ │ │ -.IP "\-t \-\-transformation=(required, input); io" │ │ │ │ +.IP "\-t \-\-transformation=(input, required); io" │ │ │ │ transformation of which the quantity will be evaluated. │ │ │ │ For supported file types see PLUGINS:3dtransform/io │ │ │ │ .RE │ │ │ │ .SS │ │ │ │ Parameters │ │ │ │ .RS │ │ │ │ .IP "\-q \-\-quantity=strain" │ │ ├── ./usr/share/man/man1/mia-3dfield2norm.1.gz │ │ │ ├── mia-3dfield2norm.1 │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-3dfield2norm \-i \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-3dfield2norm │ │ │ │ This program converts a 3d vector field to an image of its voxel-wise norm. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-vectorfield=(required, input); io" │ │ │ │ +.IP "\-i \-\-in-vectorfield=(input, required); io" │ │ │ │ input vector field │ │ │ │ For supported file types see PLUGINS:3dvf/io │ │ │ │ -.IP "\-o \-\-out-image=(required, output); io" │ │ │ │ +.IP "\-o \-\-out-image=(output, required); io" │ │ │ │ output image comprising the per voxel norm of each image │ │ │ │ For supported file types see PLUGINS:3dimage/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-3dgetsize.1.gz │ │ │ ├── mia-3dgetsize.1 │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-3dgetsize \-i [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-3dgetsize │ │ │ │ Write the dimensions of the input 3D image to stdout. │ │ │ │ .SH OPTIONS │ │ │ │ .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:3dimage/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-3dgetslice.1.gz │ │ │ ├── mia-3dgetslice.1 │ │ │ │ @@ -8,15 +8,15 @@ │ │ │ │ .B mia\-3dgetslice │ │ │ │ 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. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-in-file=(input, required); io" │ │ │ │ input image(s) to be filtered │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ +.IP "\-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 PLUGINS:2dimage/io │ │ │ │ .IP "\-t \-\-type=png" │ │ │ │ output file type for number != 1 │ │ │ │ │ │ │ │ .RS 10 │ │ │ │ .I │ │ ├── ./usr/share/man/man1/mia-3dimageaddattributes.1.gz │ │ │ ├── mia-3dimageaddattributes.1 │ │ │ │ @@ -5,21 +5,21 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-3dimageaddattributes \-i \-o \-a [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-3dimageaddattributes │ │ │ │ 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. │ │ │ │ .SH OPTIONS │ │ │ │ .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:3dimage/io │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ output image(s) with the added attributes │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ -.IP "\-a \-\-attr=(input, required); io" │ │ │ │ +.IP "\-a \-\-attr=(required, input); io" │ │ │ │ 2D image providing the attributes │ │ │ │ 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-3dimagefilterstack.1.gz │ │ │ ├── mia-3dimagefilterstack.1 │ │ │ │ @@ -8,15 +8,15 @@ │ │ │ │ .B mia\-3dimagefilterstack │ │ │ │ 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. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-in-file=(required, input); io" │ │ │ │ input image(s) to be filtered │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ +.IP "\-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 PLUGINS:3dimage/io │ │ │ │ .IP "\-t \-\-type=(required); set" │ │ │ │ output file type │ │ │ │ │ │ │ │ .RS 10 │ │ │ │ .I │ │ │ │ @@ -1134,15 +1134,15 @@ │ │ │ │ .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 │ │ │ │ -=(output, required, io) │ │ │ │ +=(required, output, io) │ │ │ │ .RS 2 │ │ │ │ name of the output file to save the image too.. │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ ├── ./usr/share/man/man1/mia-3dimageselect.1.gz │ │ │ ├── mia-3dimageselect.1 │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-3dimageselect \-i \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-3dimageselect │ │ │ │ This program is used to select one 3D images from a multi-image file. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ input images │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ -.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ output image │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ .IP "\-n \-\-number=0" │ │ │ │ image number to be selected │ │ │ │ │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ ├── ./usr/share/man/man1/mia-3dimagestatistics-in-mask.1.gz │ │ │ ├── mia-3dimagestatistics-in-mask.1 │ │ │ │ @@ -6,18 +6,18 @@ │ │ │ │ .B mia\-3dimagestatistics\-in\-mask \-i \-m [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-3dimagestatistics\-in\-mask │ │ │ │ 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. │ │ │ │ .SH OPTIONS │ │ │ │ .SS File-IO │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-image=(required, input); io" │ │ │ │ +.IP "\-i \-\-image=(input, required); io" │ │ │ │ input image to be analyzed │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ -.IP "\-m \-\-mask=(required, input); io" │ │ │ │ +.IP "\-m \-\-mask=(input, required); io" │ │ │ │ mask image to use to restrict the analysis │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ .IP "\-s \-\-summary=(output); string" │ │ │ │ File to write the summary statistics to as plain text. │ │ │ │ │ │ │ │ .IP "\-H \-\-histogram=(output); string" │ │ │ │ File to write the histogram to │ │ ├── ./usr/share/man/man1/mia-3dimagestats.1.gz │ │ │ ├── mia-3dimagestats.1 │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-3dimagestats \-i [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-3dimagestats │ │ │ │ This program is used to evaluate certain image statistics and print them out on the console. │ │ │ │ .SH OPTIONS │ │ │ │ .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:3dimage/io │ │ │ │ .IP "\-t \-\-thresh=10" │ │ │ │ intensity thresh to ignore │ │ │ │ │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ ├── ./usr/share/man/man1/mia-3disosurface-from-stack.1.gz │ │ │ ├── mia-3disosurface-from-stack.1 │ │ │ │ @@ -6,18 +6,18 @@ │ │ │ │ .B mia\-3disosurface\-from\-stack \-i \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-3disosurface\-from\-stack │ │ │ │ This program is used to extract an iso-surface from the input gray scale image given as slices. │ │ │ │ .SH OPTIONS │ │ │ │ .SS File-IO │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-image=(input, required); string" │ │ │ │ +.IP "\-i \-\-in-image=(required, input); string" │ │ │ │ input image filename pattern │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-mesh=(output, required); string" │ │ │ │ +.IP "\-o \-\-out-mesh=(required, output); string" │ │ │ │ output mesh │ │ │ │ │ │ │ │ .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-3disosurface-from-volume.1.gz │ │ │ ├── mia-3disosurface-from-volume.1 │ │ │ │ @@ -6,18 +6,18 @@ │ │ │ │ .B mia\-3disosurface\-from\-volume \-i \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-3disosurface\-from\-volume │ │ │ │ This program is used to extract an iso-surface from the input gray scale image by using marching thetrahedra. │ │ │ │ .SH OPTIONS │ │ │ │ .SS File-IO │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ input image │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ output mesh │ │ │ │ For supported file types see PLUGINS:mesh/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-3dlandmarks-transform.1.gz │ │ │ ├── mia-3dlandmarks-transform.1 │ │ │ │ @@ -5,21 +5,21 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-3dlandmarks\-transform \-i \-o \-t [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-3dlandmarks\-transform │ │ │ │ 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). │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ +.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ input landmark set │ │ │ │ For supported file types see PLUGINS:3dlandmarklist/io │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ output landmark set │ │ │ │ For supported file types see PLUGINS:3dlandmarklist/io │ │ │ │ -.IP "\-t \-\-transformation=(input, required); io" │ │ │ │ +.IP "\-t \-\-transformation=(required, input); io" │ │ │ │ transformation file │ │ │ │ For supported file types see PLUGINS:3dtransform/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-3dmany2one-nonrigid.1.gz │ │ │ ├── mia-3dmany2one-nonrigid.1 │ │ │ │ @@ -1280,15 +1280,15 @@ │ │ │ │ .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:3dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ ├── ./usr/share/man/man1/mia-3dmaskseeded.1.gz │ │ │ ├── mia-3dmaskseeded.1 │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-3dmaskseeded \-i \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-3dmaskseeded │ │ │ │ 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 neighboring point. After region growing is finished, this mask is used to zero out the region in the original image yielding the resulting image. │ │ │ │ .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:3dimage/io │ │ │ │ .IP "\-o \-\-out-file=(required, output); io" │ │ │ │ output image(s) that have been filtered │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ .IP "\-s \-\-seed=[0,0,0]" │ │ │ │ seed point │ │ ├── ./usr/share/man/man1/mia-3dmotioncompica-nonrigid.1.gz │ │ │ ├── mia-3dmotioncompica-nonrigid.1 │ │ │ │ @@ -14,15 +14,15 @@ │ │ │ │ .UE │ │ │ │ .RE │ │ │ │ │ │ │ │ . │ │ │ │ .SH OPTIONS │ │ │ │ .SS File-IO │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ input images of consecutively numbered filed (nameXXXX.ext) │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ .IP "\-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 PLUGINS:3dimage/io │ │ │ │ .IP " \-\-save-refs=" │ │ │ │ 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' │ │ ├── ./usr/share/man/man1/mia-3dnonrigidreg.1.gz │ │ │ ├── mia-3dnonrigidreg.1 │ │ │ │ @@ -70,15 +70,15 @@ │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-in-image=(required, input); io" │ │ │ │ test image │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ .IP "\-r \-\-ref-image=(required, input); io" │ │ │ │ reference image │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ -.IP "\-o \-\-out-image=(output, required); io" │ │ │ │ +.IP "\-o \-\-out-image=(required, output); io" │ │ │ │ registered output image │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ .IP "\-t \-\-transformation=(output); io" │ │ │ │ output transformation │ │ │ │ For supported file types see PLUGINS:3dtransform/io │ │ │ │ .RE │ │ │ │ .SS Processing │ │ │ │ @@ -1281,15 +1281,15 @@ │ │ │ │ .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 │ │ │ │ -=(output, required, io) │ │ │ │ +=(required, output, io) │ │ │ │ .RS 2 │ │ │ │ name of the output file to save the image too.. │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ ├── ./usr/share/man/man1/mia-3dprealign-nonrigid.1.gz │ │ │ ├── mia-3dprealign-nonrigid.1 │ │ │ │ @@ -17,15 +17,15 @@ │ │ │ │ .SH OPTIONS │ │ │ │ .SS │ │ │ │ File-IO │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-in-file=(input, required); io" │ │ │ │ input images following the naming pattern nameXXXX.ext │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ file name base for registered files given as C\-format string │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ .IP " \-\-save-references" │ │ │ │ Save synthetic references to files refXXXX.v │ │ │ │ │ │ │ │ .RE │ │ │ │ .SS │ │ │ │ @@ -1321,15 +1321,15 @@ │ │ │ │ .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 │ │ │ │ -=(output, required, io) │ │ │ │ +=(required, output, io) │ │ │ │ .RS 2 │ │ │ │ name of the output file to save the image too.. │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ ├── ./usr/share/man/man1/mia-3dpropose-boundingbox.1.gz │ │ │ ├── mia-3dpropose-boundingbox.1 │ │ │ │ @@ -6,15 +6,15 @@ │ │ │ │ .B mia\-3dpropose\-boundingbox \-i [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-3dpropose\-boundingbox │ │ │ │ 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. │ │ │ │ .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:3dimage/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: │ │ │ │ @@ -271,15 +271,15 @@ │ │ │ │ .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:3dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ @@ -585,15 +585,15 @@ │ │ │ │ lower threshold for mask growing. │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ ref │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ reference image for mask region growing. │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ @@ -666,15 +666,15 @@ │ │ │ │ .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 │ │ │ │ @@ -692,15 +692,15 @@ │ │ │ │ .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:3dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ @@ -719,15 +719,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B 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: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ input │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ second input image file name. │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ @@ -1109,15 +1109,15 @@ │ │ │ │ For supported plug-ins see PLUGINS:3dimage/shape │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ seed │ │ │ │ -=(input, required, string) │ │ │ │ +=(required, input, string) │ │ │ │ .RS 2 │ │ │ │ seed input image containing the labels for the initial regions. │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ .B tee │ │ │ │ @@ -1143,15 +1143,15 @@ │ │ │ │ .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:3dtransform/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ ├── ./usr/share/man/man1/mia-3dsegment-ahmed.1.gz │ │ │ ├── mia-3dsegment-ahmed.1 │ │ │ │ @@ -17,15 +17,15 @@ │ │ │ │ changes are: p=2, and exp │ │ │ │ .SH OPTIONS │ │ │ │ .SS File-IO │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-in-file=(input, required); io" │ │ │ │ image to be segmented │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ -.IP "\-c \-\-class-file=(required, output); io" │ │ │ │ +.IP "\-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 PLUGINS:3dimage/io │ │ │ │ .IP "\-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 PLUGINS:3dimage/io │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ ├── ./usr/share/man/man1/mia-3dsegment-local-cmeans.1.gz │ │ │ ├── mia-3dsegment-local-cmeans.1 │ │ │ │ @@ -13,15 +13,15 @@ │ │ │ │ Dunmore CJ, Wollny G, Skinner MM. (2018) MIA-Clustering: a novel method for segmentation of paleontological material. PeerJ 6:e4374. │ │ │ │ .UE │ │ │ │ .RE │ │ │ │ │ │ │ │ .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:3dimage/io │ │ │ │ .IP "\-o \-\-out-file=(output); io" │ │ │ │ class label image based on merging local labels │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ .IP "\-G \-\-out-global-crisp=(output); io" │ │ │ │ class label image based on global segmentation │ │ ├── ./usr/share/man/man1/mia-3dseries-track-intensity.1.gz │ │ │ ├── mia-3dseries-track-intensity.1 │ │ │ │ @@ -7,18 +7,18 @@ │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-3dseries\-track\-intensity │ │ │ │ This program tracks the intensity of a pixel at the given coordinates. │ │ │ │ .SH OPTIONS │ │ │ │ .SS │ │ │ │ File-IO │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ input perfusion data set │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ -.IP "\-o \-\-out-file=(required, output); string" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); string" │ │ │ │ file name for output intensity slopes │ │ │ │ │ │ │ │ .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-3dtrackpixelmovement.1.gz │ │ │ ├── mia-3dtrackpixelmovement.1 │ │ │ │ @@ -13,15 +13,15 @@ │ │ │ │ .SH OPTIONS │ │ │ │ .SS │ │ │ │ File-IO │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-in-file=(input, required); string" │ │ │ │ input point set │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(output, required); string" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); string" │ │ │ │ output point set │ │ │ │ │ │ │ │ .IP "\-t \-\-transformation=(input, required); io" │ │ │ │ transformation describing the monitored change │ │ │ │ For supported file types see PLUGINS:3dtransform/io │ │ │ │ .RE │ │ │ │ .SS │ │ ├── ./usr/share/man/man1/mia-3dtransform2vf.1.gz │ │ │ ├── mia-3dtransform2vf.1 │ │ │ │ @@ -8,15 +8,15 @@ │ │ │ │ .B mia\-3dtransform2vf │ │ │ │ Create a 3D vector field from a given transformation. The output vector field will have the dimesions as given in the transformation description. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-in-file=(input, required); io" │ │ │ │ input transformation │ │ │ │ For supported file types see PLUGINS:3dtransform/io │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ output vector field │ │ │ │ For supported file types see PLUGINS:3dvf/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-3dvectorfieldcreate.1.gz │ │ │ ├── mia-3dvectorfieldcreate.1 │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-3dvectorfieldcreate \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-3dvectorfieldcreate │ │ │ │ This program is used to create a file containing a 3D vector field. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ output file for the vector field │ │ │ │ For supported file types see PLUGINS:3dvf/io │ │ │ │ .IP "\-s \-\-size=[64,64,64]" │ │ │ │ size of the vector field │ │ │ │ │ │ │ │ .IP "\-y \-\-ftype=0" │ │ │ │ vector field type │ │ ├── ./usr/share/man/man1/mia-3dvf2transform.1.gz │ │ │ ├── mia-3dvf2transform.1 │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-3dvf2transform \-i \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-3dvf2transform │ │ │ │ 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. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ input transformation │ │ │ │ For supported file types see PLUGINS:3dvf/io │ │ │ │ .IP "\-o \-\-out-file=(output, required); io" │ │ │ │ output vector field │ │ │ │ For supported file types see PLUGINS:3dtransform/io │ │ │ │ .IP "\-k \-\-imgkernel=bspline:d=3" │ │ │ │ image interpolator kernel which is used when the transformation is applied to an image │ │ ├── ./usr/share/man/man1/mia-labelsort.1.gz │ │ │ ├── mia-labelsort.1 │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-labelsort \-i \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-labelsort │ │ │ │ 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. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ input file name containing the histogram │ │ │ │ │ │ │ │ .IP "\-o \-\-out-file=(required, output); string" │ │ │ │ output file name to store probabilities │ │ │ │ │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ ├── ./usr/share/man/man1/mia-mesh-deformable-model.1.gz │ │ │ ├── mia-mesh-deformable-model.1 │ │ │ │ @@ -6,21 +6,21 @@ │ │ │ │ .B mia\-mesh\-deformable\-model \-i \-o \-r [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-mesh\-deformable\-model │ │ │ │ This program runs a deformable model to adapt a mesh to an iso-value within a given image. │ │ │ │ .SH OPTIONS │ │ │ │ .SS File I/O │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ input mesh to be adapted │ │ │ │ For supported file types see PLUGINS:mesh/io │ │ │ │ .IP "\-o \-\-out-file=(required, output); io" │ │ │ │ output mesh that has been deformed │ │ │ │ For supported file types see PLUGINS:mesh/io │ │ │ │ -.IP "\-r \-\-ref-file=(required, input); io" │ │ │ │ +.IP "\-r \-\-ref-file=(input, required); io" │ │ │ │ reference image │ │ │ │ For supported file types see PLUGINS:3dimage/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: │ │ │ │ @@ -301,15 +301,15 @@ │ │ │ │ .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:3dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ @@ -615,15 +615,15 @@ │ │ │ │ lower threshold for mask growing. │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ ref │ │ │ │ -=(required, input, io) │ │ │ │ +=(input, required, io) │ │ │ │ .RS 2 │ │ │ │ reference image for mask region growing. │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ @@ -696,15 +696,15 @@ │ │ │ │ .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 │ │ │ │ @@ -722,15 +722,15 @@ │ │ │ │ .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:3dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ @@ -749,15 +749,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B 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: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ input │ │ │ │ -=(required, input, io) │ │ │ │ +=(input, required, io) │ │ │ │ .RS 2 │ │ │ │ second input image file name. │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ @@ -1139,15 +1139,15 @@ │ │ │ │ For supported plug-ins see PLUGINS:3dimage/shape │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ seed │ │ │ │ -=(required, input, string) │ │ │ │ +=(input, required, string) │ │ │ │ .RS 2 │ │ │ │ seed input image containing the labels for the initial regions. │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ .B tee │ │ │ │ @@ -1173,15 +1173,15 @@ │ │ │ │ .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:3dtransform/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ ├── ./usr/share/man/man1/mia-mesh-to-maskimage.1.gz │ │ │ ├── mia-mesh-to-maskimage.1 │ │ │ │ @@ -9,15 +9,15 @@ │ │ │ │ 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. │ │ │ │ .SH OPTIONS │ │ │ │ .SS File I/O │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-in-file=(required, input); io" │ │ │ │ input mesh to be adapted │ │ │ │ For supported file types see PLUGINS:mesh/io │ │ │ │ -.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ output image containing the binary mask │ │ │ │ For supported file types see PLUGINS:3dimage/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-meshfilter.1.gz │ │ │ ├── mia-meshfilter.1 │ │ │ │ @@ -7,18 +7,18 @@ │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-meshfilter │ │ │ │ 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 │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ +.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ input mesh to be filtered │ │ │ │ For supported file types see PLUGINS:mesh/io │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ output mesh that have been filtered │ │ │ │ For supported file types see PLUGINS:mesh/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-multihist.1.gz │ │ │ ├── mia-multihist.1 │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-multihist \-i \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-multihist │ │ │ │ This program evaluates the histogram over a series of 2D images │ │ │ │ .SH OPTIONS │ │ │ │ .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-histogram=(required, output); string" │ │ │ │ output file name │ │ │ │ │ │ │ │ .IP " \-\-min=0" │ │ │ │ minimum of histogram range │ │ ├── ./usr/share/man/man1/mia-myowavelettest.1.gz │ │ │ ├── mia-myowavelettest.1 │ │ │ │ @@ -6,15 +6,15 @@ │ │ │ │ .B mia\-myowavelettest \-i [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-myowavelettest │ │ │ │ This program runs the wavelet based slope-statistics on the mixing matrix of a ICA perfusion series. │ │ │ │ .SH OPTIONS │ │ │ │ .SS File-IO │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ +.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ input data set │ │ │ │ │ │ │ │ .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-raw2image.1.gz │ │ │ ├── mia-raw2image.1 │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-raw2image \-i \-o \-s [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-raw2image │ │ │ │ This program is used to convert raw data to a 2D file format. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ input file name │ │ │ │ │ │ │ │ .IP "\-o \-\-out-file=(output, required); io" │ │ │ │ output file name │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-r \-\-repn=ubyte" │ │ │ │ input pixel type │ │ ├── ./usr/share/man/man1/mia-wavelettrans.1.gz │ │ │ ├── mia-wavelettrans.1 │ │ │ │ @@ -9,15 +9,15 @@ │ │ │ │ This program runs the a column-wise discret wavelet forward transform on the data given by an input text file. │ │ │ │ .SH OPTIONS │ │ │ │ .SS File-IO │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-in-file=(input, required); string" │ │ │ │ input data set │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(required, output); string" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); string" │ │ │ │ output data set │ │ │ │ │ │ │ │ .IP "\-s \-\-save-wave=(output); string" │ │ │ │ base name of the output files that will store the wavelet coefficients as matrix │ │ │ │ │ │ │ │ .RE │ │ │ │ .SS Help & Info