--- /srv/rebuilderd/tmp/rebuilderd6Jdiu2/inputs/mia-tools_2.4.7-16_i386.deb +++ /srv/rebuilderd/tmp/rebuilderd6Jdiu2/out/mia-tools_2.4.7-16_i386.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 7564 2025-10-24 23:01:09.000000 control.tar.xz │ --rw-r--r-- 0 0 0 1969252 2025-10-24 23:01:09.000000 data.tar.xz │ +-rw-r--r-- 0 0 0 7560 2025-10-24 23:01:09.000000 control.tar.xz │ +-rw-r--r-- 0 0 0 1969276 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/ │ │ │ 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./usr/share/man/man1/mia-2dimageregistration.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1491 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) 1956 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) 3668 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dmany2one-nonrigid.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 2776 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dmulti-force.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 3675 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dmany2one-nonrigid.1.gz │ 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│ │ +-rw-r--r-- 0 root (0) root (0) 982 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dsegcompare.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 988 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dseghausdorff.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1793 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dsegment-ahmed.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 6321 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dsegment-fuzzyw.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1791 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dsegment-ahmed.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 6322 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dsegment-fuzzyw.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 2309 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dsegment-local-cmeans.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1903 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dsegment-local-kmeans.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1839 2025-10-24 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./usr/share/man/man1/mia-2dto3dimage.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1888 2025-10-24 23:01:09.000000 ./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) 1668 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dtransform.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1371 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) 1118 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) 1879 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dbrainextractT1.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1634 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dbinarycombine.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1881 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dbrainextractT1.1.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) 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) 3430 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dcost-translatedgrad.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 6737 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) 1650 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) 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) 1869 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) 1141 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3ddistance.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1875 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3deval-transformquantity.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) 3575 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) 1144 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) 1673 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dfield2norm.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 3572 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) 2318 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dfluid.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 2367 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dforce.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 2368 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dforce.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1705 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) 1469 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) 1970 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dimageaddattributes.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) 1906 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dimagecreator.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 5697 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dimagefilter.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) 1548 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dimageselect.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1929 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) 1269 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) 2262 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) 1719 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dlerp.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 7895 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) 2558 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) 2562 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dmotioncompica-nonrigid.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 9544 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) 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) 10015 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dprealign-nonrigid.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 5800 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dpropose-boundingbox.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 5107 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3drigidreg.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) 1931 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dsegment-ahmed.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 2574 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) 9442 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) 1368 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) 1314 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) 1657 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dvf2transform.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1268 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dvfcompare.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1120 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-cmeans.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 882 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-filenumberpattern.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 987 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) 2143 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) 883 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-filenumberpattern.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) 6459 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) 2139 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) 2437 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) 2435 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) 1737 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) 1736 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-raw2image.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1807 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-raw2volume.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 │ │ │ │ @@ -5,21 +5,21 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dbinarycombine \-1 \-2 \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dbinarycombine │ │ │ │ This program is used to combine two binary images by some kind of operation. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-1 \-\-file1=(input, required); io" │ │ │ │ +.IP "\-1 \-\-file1=(required, input); io" │ │ │ │ input mask image 1 │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-2 \-\-file2=(input, required); io" │ │ │ │ +.IP "\-2 \-\-file2=(required, input); 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-2ddeform.1.gz │ │ │ ├── mia-2ddeform.1 │ │ │ │ @@ -8,15 +8,15 @@ │ │ │ │ .B mia\-2ddeform │ │ │ │ This program is used to deform a 2D image using a deformation vector field. Input image and deformation field must be of the same size. The transformation formula is 'x -> x - v(x)' │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-in-file=(input, required); io" │ │ │ │ input image │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ transformed image │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-t \-\-transformation=(input, required); io" │ │ │ │ transformation vector field │ │ │ │ For supported file types see PLUGINS:2dvf/io │ │ │ │ .IP "\-p \-\-interpolator=bspline:d=3" │ │ │ │ image interpolator kernel │ │ ├── ./usr/share/man/man1/mia-2ddistance.1.gz │ │ │ ├── mia-2ddistance.1 │ │ │ │ @@ -11,15 +11,15 @@ │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-in-file=(required, input); io" │ │ │ │ input image │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-d \-\-distance-file=(required, input); io" │ │ │ │ distance field image (floating point) │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-o \-\-out-file=(output, required); string" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); string" │ │ │ │ output file, '\-': write to stdout │ │ │ │ │ │ │ │ .IP "\-s \-\-scale=1" │ │ │ │ distance scaling factor │ │ │ │ │ │ │ │ .IP "\-m \-\-method=avg" │ │ │ │ distance measuring method │ │ ├── ./usr/share/man/man1/mia-2deval-transformquantity.1.gz │ │ │ ├── mia-2deval-transformquantity.1 │ │ │ │ @@ -27,15 +27,15 @@ │ │ │ │ .SH OPTIONS │ │ │ │ .SS │ │ │ │ File-IO │ │ │ │ .RS │ │ │ │ .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=(input, required); io" │ │ │ │ transformation of which the quantity will be evaluated. │ │ │ │ For supported file types see PLUGINS:2dtransform/io │ │ │ │ .RE │ │ │ │ .SS │ │ ├── ./usr/share/man/man1/mia-2dforce.1.gz │ │ │ ├── mia-2dforce.1 │ │ │ │ @@ -5,21 +5,21 @@ │ │ │ │ .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" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ output force norm image │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-c \-\-cost=(required); string" │ │ │ │ cost function to use │ │ │ │ │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ ├── ./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=(required, input); io" │ │ │ │ +.IP "\-1 \-\-in-file-1=(input, required); io" │ │ │ │ input image 1 │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-2 \-\-in-file-2=(required, input); io" │ │ │ │ +.IP "\-2 \-\-in-file-2=(input, required); io" │ │ │ │ input image 2 │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ │ │ .RS │ │ │ │ .IP "\-V \-\-verbose=warning" │ │ │ │ verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are: │ │ ├── ./usr/share/man/man1/mia-2dimagecombiner.1.gz │ │ │ ├── mia-2dimagecombiner.1 │ │ │ │ @@ -5,21 +5,21 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dimagecombiner \-1 \-2 \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dimagecombiner │ │ │ │ Combine two image by a given operation. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-1 \-\-in-file-1=(required, input); io" │ │ │ │ +.IP "\-1 \-\-in-file-1=(input, required); io" │ │ │ │ first input image to be combined │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-2 \-\-in-file-2=(required, input); io" │ │ │ │ +.IP "\-2 \-\-in-file-2=(input, required); io" │ │ │ │ second input image to be combined │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ output image(s) that have been filtered │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-p \-\-operation=absdiff" │ │ │ │ operation to be applied │ │ │ │ For supported plugins see PLUGINS:2dimage/combiner │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ ├── ./usr/share/man/man1/mia-2dimagecreator.1.gz │ │ │ ├── mia-2dimagecreator.1 │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dimagecreator \-o \-j [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dimagecreator │ │ │ │ This program is used to create test images. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ output file for create object │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-s \-\-size=[128,128]" │ │ │ │ size of the object │ │ │ │ │ │ │ │ .IP "\-r \-\-repn=ubyte" │ │ │ │ input pixel type │ │ ├── ./usr/share/man/man1/mia-2dimageregistration.1.gz │ │ │ ├── mia-2dimageregistration.1 │ │ │ │ @@ -6,24 +6,24 @@ │ │ │ │ .B mia\-2dimageregistration \-i \-r \-t [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dimageregistration │ │ │ │ This program runs registration of two images optimizing a transformation of the given transformation model by optimizing certain cost measures that are given as free parameters. │ │ │ │ .SH OPTIONS │ │ │ │ .SS File-IO │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-image=(required, input); io" │ │ │ │ +.IP "\-i \-\-in-image=(input, required); io" │ │ │ │ test image to be registered │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-r \-\-ref-image=(required, input); io" │ │ │ │ +.IP "\-r \-\-ref-image=(input, required); io" │ │ │ │ reference image to be registered to │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-o \-\-out-image=(output); io" │ │ │ │ registered output image │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-t \-\-transformation=(required, output); io" │ │ │ │ +.IP "\-t \-\-transformation=(output, required); io" │ │ │ │ output transformation comprising the registration │ │ │ │ For supported file types see PLUGINS:2dtransform/io │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ │ │ .RS │ │ │ │ .IP "\-V \-\-verbose=warning" │ │ │ │ verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are: │ │ ├── ./usr/share/man/man1/mia-2dimageselect.1.gz │ │ │ ├── mia-2dimageselect.1 │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dimageselect \-i \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .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" │ │ │ │ +.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ input images │ │ │ │ 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 "\-n \-\-number=0" │ │ │ │ image number to be selected │ │ ├── ./usr/share/man/man1/mia-2dimageseries-maximum-intensity-projection.1.gz │ │ │ ├── mia-2dimageseries-maximum-intensity-projection.1 │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dimageseries\-maximum\-intensity\-projection \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dimageseries\-maximum\-intensity\-projection │ │ │ │ This program is used to evaluate the per-pixel maximum intensity of an image series. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ output image │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ │ │ .RS │ │ │ │ .IP "\-V \-\-verbose=warning" │ │ │ │ verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are: │ │ ├── ./usr/share/man/man1/mia-2dimagestack-cmeans.1.gz │ │ │ ├── mia-2dimagestack-cmeans.1 │ │ │ │ @@ -6,15 +6,15 @@ │ │ │ │ .B mia\-2dimagestack\-cmeans \-i \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dimagestack\-cmeans │ │ │ │ This program first evaluates a sparse histogram of an input image series, then runs a c-means classification over the histogram and then writes the probability mapping for thr original intensity values │ │ │ │ .SH OPTIONS │ │ │ │ .SS File-IO │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(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-probmap=(output, required); string" │ │ │ │ Save probability map to this file │ │ │ │ │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ ├── ./usr/share/man/man1/mia-2dimagestats.1.gz │ │ │ ├── mia-2dimagestats.1 │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dimagestats \-i [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dimagestats │ │ │ │ This progranm is used to evaluate some statistics of an image. Output is Mean, Variation, Median, and Median Average Distance of the intensity values. The program allows one to set a lower threshold and to cut off a percentage of the high intensity pixels │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ +.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ input image to be analyzed │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-t \-\-thresh=10" │ │ │ │ intensity thresh to ignore │ │ │ │ │ │ │ │ .IP "\-g \-\-high-thresh=0.05" │ │ │ │ upper histogram percentage to ignore │ │ ├── ./usr/share/man/man1/mia-2dmany2one-nonrigid.1.gz │ │ │ ├── mia-2dmany2one-nonrigid.1 │ │ │ │ @@ -7,15 +7,15 @@ │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dmany2one\-nonrigid │ │ │ │ This program registers all images of a conscutively numbered set of images to one common user defined reference. │ │ │ │ .SH OPTIONS │ │ │ │ .SS │ │ │ │ File-IO │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ +.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ input perfusion data set │ │ │ │ │ │ │ │ .IP "\-o \-\-out-file=(output, required); string" │ │ │ │ file name for registered images, numbering and pattern are deducted from the input data │ │ │ │ │ │ │ │ .RE │ │ │ │ .SS │ │ ├── ./usr/share/man/man1/mia-2dmulti-force.1.gz │ │ │ ├── mia-2dmulti-force.1 │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dmulti\-force \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dmulti\-force │ │ │ │ This program evaluates the 2D image cost force norm image of a given cost function set. The input images must be of the same dimensions and gray scale (whatever bit-depth). │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ output norm image │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ │ │ .RS │ │ │ │ .IP "\-V \-\-verbose=warning" │ │ │ │ verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are: │ │ ├── ./usr/share/man/man1/mia-2dmultiimageto3d.1.gz │ │ │ ├── mia-2dmultiimageto3d.1 │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dmultiimageto3d \-i \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dmultiimageto3d │ │ │ │ This program is used to convert a 2D multi-image file to a 3D image. │ │ │ │ .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:2dimage/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 │ │ │ │ .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-2dmyocard-segment.1.gz │ │ │ ├── mia-2dmyocard-segment.1 │ │ │ │ @@ -6,18 +6,18 @@ │ │ │ │ .B mia\-2dmyocard\-segment \-i \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dmyocard\-segment │ │ │ │ This program is work in progress │ │ │ │ .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); io" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ output myocardial mask │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-f \-\-save-features=(output); string" │ │ │ │ save ICA features to files with this name base │ │ │ │ │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ ├── ./usr/share/man/man1/mia-2dmyoica-nonrigid-parallel.1.gz │ │ │ ├── mia-2dmyoica-nonrigid-parallel.1 │ │ │ │ @@ -14,15 +14,15 @@ │ │ │ │ .UE │ │ │ │ .RE │ │ │ │ │ │ │ │ This version of the program runs all registrations in parallel. │ │ │ │ .SH OPTIONS │ │ │ │ .SS File-IO │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ input perfusion data set │ │ │ │ │ │ │ │ .IP "\-o \-\-out-file=(output, required); string" │ │ │ │ output perfusion data set │ │ │ │ │ │ │ │ .IP "\-r \-\-registered=reg" │ │ │ │ File name base for the registered images. Image type and numbering scheme are taken from the input images as given in the input data set. │ │ ├── ./usr/share/man/man1/mia-2dmyoica-nonrigid.1.gz │ │ │ ├── mia-2dmyoica-nonrigid.1 │ │ │ │ @@ -13,18 +13,18 @@ │ │ │ │ Wollny G, Kellman P, Santos A, Ledesma-Carbayo M-J, "Automatic Motion Compensation of Free Breathing acquired Myocardial Perfusion Data by using Independent Component Analysis" Medical Image Analysis, 2012. │ │ │ │ .UE │ │ │ │ .RE │ │ │ │ │ │ │ │ .SH OPTIONS │ │ │ │ .SS File-IO │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ +.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ input perfusion data set │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(output, required); string" │ │ │ │ +.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 │ │ │ │ @@ -8,18 +8,18 @@ │ │ │ │ .B mia\-2dmyoica\-nonrigid2 │ │ │ │ This program runs the non-rigid registration of an perfusion image series.In each pass, first an ICA analysis is run to estimate and eliminate the periodic movement and create reference images with intensities similar to the corresponding original image. Then non-rigid registration is run using the an "ssd + divcurl" cost model. The B-spline c-rate and the divcurl cost weight are changed in each pass according to given parameters.In the first pass a bounding box around the LV myocardium may be extractedto speed up computation │ │ │ │ Special note to this implemnentation: the registration is always run from the original images to avoid the accumulation of interpolation errors. │ │ │ │ .SH OPTIONS │ │ │ │ .SS │ │ │ │ File-IO │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ +.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ input perfusion data set │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(output, required); string" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); string" │ │ │ │ output perfusion data set │ │ │ │ │ │ │ │ .IP "\-r \-\-registered=reg" │ │ │ │ file name base for registered fiels │ │ │ │ │ │ │ │ .IP " \-\-save-cropped=" │ │ │ │ save cropped set to this file │ │ ├── ./usr/share/man/man1/mia-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=(required, output); string" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); 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=(required, output); string" │ │ │ │ output perfusion data set │ │ │ │ │ │ │ │ .IP "\-r \-\-registered=" │ │ │ │ file name base for registered files │ │ ├── ./usr/share/man/man1/mia-2dmyoperiodic-nonrigid.1.gz │ │ │ ├── mia-2dmyoperiodic-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=(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-references" │ │ │ │ Save synthetic references to files refXXXX.v │ │ ├── ./usr/share/man/man1/mia-2dmyopgt-nonrigid.1.gz │ │ │ ├── mia-2dmyopgt-nonrigid.1 │ │ │ │ @@ -19,15 +19,15 @@ │ │ │ │ .SH OPTIONS │ │ │ │ .SS │ │ │ │ File-IO │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-in-file=(required, input); string" │ │ │ │ input perfusion data set │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(required, output); string" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); string" │ │ │ │ output perfusion data set │ │ │ │ │ │ │ │ .IP "\-r \-\-registered=reg" │ │ │ │ file name base for registered files, the image file type is the same as given in the input data set │ │ │ │ │ │ │ │ .RE │ │ │ │ .SS │ │ ├── ./usr/share/man/man1/mia-2dmyoserial-nonrigid.1.gz │ │ │ ├── mia-2dmyoserial-nonrigid.1 │ │ │ │ @@ -14,18 +14,18 @@ │ │ │ │ .UE │ │ │ │ .RE │ │ │ │ │ │ │ │ .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" │ │ │ │ +.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-compdice.1.gz │ │ │ ├── mia-2dmyoseries-compdice.1 │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dmyoseries\-compdice \-1 \-2 [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dmyoseries\-compdice │ │ │ │ This program is used to evaluate the per-frame dice index of segmented regions of two image series │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-1 \-\-first=(input, required); string" │ │ │ │ +.IP "\-1 \-\-first=(required, input); string" │ │ │ │ first segmentation set │ │ │ │ │ │ │ │ -.IP "\-2 \-\-second=(input, required); string" │ │ │ │ +.IP "\-2 \-\-second=(required, input); string" │ │ │ │ second segmentation set │ │ │ │ │ │ │ │ .IP "\-k \-\-skip=2" │ │ │ │ images to skip atthe begin of the series │ │ │ │ │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ ├── ./usr/share/man/man1/mia-2dmyoseries-dice.1.gz │ │ │ ├── mia-2dmyoseries-dice.1 │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dmyoseries\-dice \-i [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dmyoseries\-dice │ │ │ │ This program is used to evaluate the per-frame dice index of segmented regions of an image with respect to the segmentation of a reference frame from the same series. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-input=(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=(output, required); string" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); string" │ │ │ │ output perfusion data set │ │ │ │ │ │ │ │ .IP " \-\-out-filebase=reg" │ │ │ │ file name basae for registered files, file type is deducted from the image file type in the input data set. │ │ │ │ │ │ │ │ .RE │ │ │ │ .SS │ │ ├── ./usr/share/man/man1/mia-2dsegcompare.1.gz │ │ │ ├── mia-2dsegcompare.1 │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dsegcompare \-i \-r [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dsegcompare │ │ │ │ This program is used to evaluate the Hausdorff distance between each frame of a perfusion time series of the input set to the corresponding frame of the reference set and prints the result to stdout. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ +.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ input segmentation set │ │ │ │ │ │ │ │ -.IP "\-r \-\-ref-file=(input, required); string" │ │ │ │ +.IP "\-r \-\-ref-file=(required, input); string" │ │ │ │ reference segmentation 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-2dseghausdorff.1.gz │ │ │ ├── mia-2dseghausdorff.1 │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dseghausdorff \-i \-r [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dseghausdorff │ │ │ │ Get the per-slice Hausdorff distance of a segmentation with respect to a given reference frame and print it to stdout. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ input segmentation set │ │ │ │ │ │ │ │ .IP "\-r \-\-ref-frame=(required); uint" │ │ │ │ reference frame │ │ │ │ │ │ │ │ .IP "\-k \-\-skip=0" │ │ │ │ skip frames at the beginning │ │ ├── ./usr/share/man/man1/mia-2dsegment-ahmed.1.gz │ │ │ ├── mia-2dsegment-ahmed.1 │ │ │ │ @@ -13,18 +13,18 @@ │ │ │ │ Mohamed N. Ahmed et. al, "A Modified Fuzzy C-Means Algorithm for Bias Field estimation and Segmentation of MRI Data", IEEE Trans. on Medical Imaging, Vol. 21, No. 3, March 2002, │ │ │ │ .UE │ │ │ │ .RE │ │ │ │ │ │ │ │ changes are: p=2, and exp │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ image to be segmented │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ class probability images, the image type must support multiple images and floating point values │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-a \-\-no-of-classes=3" │ │ │ │ number of classes │ │ │ │ │ │ │ │ .IP "\-b \-\-bias-correct" │ │ │ │ apply bias field correction │ │ ├── ./usr/share/man/man1/mia-2dsegment-fuzzyw.1.gz │ │ │ ├── mia-2dsegment-fuzzyw.1 │ │ │ │ @@ -852,15 +852,15 @@ │ │ │ │ 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 │ │ │ │ @@ -888,15 +888,15 @@ │ │ │ │ .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 │ │ │ │ @@ -1207,15 +1207,15 @@ │ │ │ │ .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-2dsegmentcropbox.1.gz │ │ │ ├── mia-2dsegmentcropbox.1 │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dsegmentcropbox \-i \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dsegmentcropbox │ │ │ │ This program is used on a segmentation set and evaluates a bounding box that encloses the segmentation in all slices. This bounding box is then used to crop the original images, correct the segmentation and store a new segmentation set with the cropped images. The cropped images will be of the same type as the original images. If no segmentation is given in the set, the result is undefined. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ +.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" │ │ │ │ output segmentation set │ │ ├── ./usr/share/man/man1/mia-2dsegseriesstats.1.gz │ │ │ ├── mia-2dsegseriesstats.1 │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dsegseriesstats \-o \-g [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dsegseriesstats │ │ │ │ This program is used evaluate various time-intensity curves over a series of images given by a segmentation set. Specifically, the program is tailored to evaluate average intensities and variations of sections the left ventricle myocardium. The segmentation set must contain the segmentations for all slices that will be accessed during evaluation. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-o \-\-original=(required, input); string" │ │ │ │ +.IP "\-o \-\-original=(input, required); string" │ │ │ │ original segmentation set │ │ │ │ │ │ │ │ -.IP "\-g \-\-registered=(required, input); string" │ │ │ │ +.IP "\-g \-\-registered=(input, required); string" │ │ │ │ registered segmentation set │ │ │ │ │ │ │ │ .IP "\-k \-\-skip=2" │ │ │ │ images to skip at the begin of the series, if (k < 0) use RV peak of the registered set if set │ │ │ │ │ │ │ │ .IP "\-r \-\-reference=\-1" │ │ │ │ reference frame for automatic curve extraction. Negative values can be used to indicate specific values (if given in the segmentation set): │ │ ├── ./usr/share/man/man1/mia-2dsegshift.1.gz │ │ │ ├── mia-2dsegshift.1 │ │ │ │ @@ -8,15 +8,15 @@ │ │ │ │ .B mia\-2dsegshift │ │ │ │ This program move the segmentation(s) of an image series by using a shift that is equal for all slices. The program also may remove images from the begin of the series. The program can be used to correct the segmentation of the images if the images where cropped. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-in-file=(input, required); io" │ │ │ │ input segmentation set │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ input segmentation set │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-g \-\-image-file=crop" │ │ │ │ output image filename base │ │ │ │ │ │ │ │ .IP "\-S \-\-shift=[0,0]" │ │ │ │ shift of segmentation │ │ ├── ./usr/share/man/man1/mia-2dsegshiftperslice.1.gz │ │ │ ├── mia-2dsegshiftperslice.1 │ │ │ │ @@ -8,15 +8,15 @@ │ │ │ │ .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" │ │ │ │ input segmentation set │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(output, required); string" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); string" │ │ │ │ output segmentation set │ │ │ │ │ │ │ │ .IP "\-g \-\-image-file=crop" │ │ │ │ output image filename base │ │ │ │ │ │ │ │ .IP "\-S \-\-shift=(required); string" │ │ │ │ shift of segmentation \- base name │ │ ├── ./usr/share/man/man1/mia-2dseries-mincorr.1.gz │ │ │ ├── mia-2dseries-mincorr.1 │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ .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=(input, required); string" │ │ │ │ +.IP "\-i \-\-in-set=(required, input); string" │ │ │ │ input segmentation set │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-set=(output, required); io" │ │ │ │ +.IP "\-o \-\-out-set=(required, output); io" │ │ │ │ output image of minimal correlation │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-k \-\-skip=2" │ │ │ │ skip images at beginning of series │ │ │ │ │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ ├── ./usr/share/man/man1/mia-2dseries-sectionmask.1.gz │ │ │ ├── mia-2dseries-sectionmask.1 │ │ │ │ @@ -8,15 +8,15 @@ │ │ │ │ .B mia\-2dseries\-sectionmask │ │ │ │ Evaluate the masks for the sections of a segmented frame. │ │ │ │ .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 containing the mask │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-f \-\-frame=0" │ │ │ │ Frame number for which to extract the mask │ │ │ │ │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ ├── ./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=(required, output); io" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ output image name │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-k \-\-skip=0" │ │ │ │ Skip files at the beginning │ │ │ │ │ │ │ │ .IP "\-e \-\-enlarge-boundary=5" │ │ │ │ Enlarge cropbox by number of pixels │ │ │ │ @@ -842,15 +842,15 @@ │ │ │ │ Intensity thresholding parameter: Pixels with intensities below this threshold will be set to zero, and also not used when evaluating mean and variation. │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ varfile │ │ │ │ -=(required, output, io) │ │ │ │ +=(output, required, io) │ │ │ │ .RS 2 │ │ │ │ name of the output file to save the variation image too.. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ @@ -878,15 +878,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B medianmad │ │ │ │ Filter that evaluates simultaniously the pixel wise median and the median absolute deviation (MAD) of an image in a given window. Pixel intensities below the given threshold will be ignored and at their loctions the output median and MAD are set to zero. The median intensity image is directly passed to the pipeline, the variation image is saved to a file given with the varfile parameter. Both output images have the same pixel type like the input image., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ madfile │ │ │ │ -=(required, output, io) │ │ │ │ +=(output, required, io) │ │ │ │ .RS 2 │ │ │ │ name of the output file to save the median absolute deviation image too.. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ @@ -1197,15 +1197,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B tee │ │ │ │ Save the input image to a file and also pass it through to the next filter, supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ file │ │ │ │ -=(required, output, io) │ │ │ │ +=(output, required, io) │ │ │ │ .RS 2 │ │ │ │ name of the output file to save the image too.. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ ├── ./usr/share/man/man1/mia-2dseries2sets.1.gz │ │ │ ├── mia-2dseries2sets.1 │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dseries2sets \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dseries2sets │ │ │ │ This program takes all image files that are given as free parameters on the command line and creates segmentation sets based on information found in the images. Used information is the z-location of the slice and the acquisition number. The code is tailored to use the according descriptors defined in the DICOM standard. All images with the same slice location will be grouped together in one segmentation set and ordered according to their acquisition number. Slice locations are rounded to three digits accuracy to make proper comparison of floating point values feasible. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-o \-\-out-directory=(required, output); string" │ │ │ │ +.IP "\-o \-\-out-directory=(output, required); string" │ │ │ │ output directory (needs to exist and be writable) │ │ │ │ │ │ │ │ .IP " \-\-no-copy" │ │ │ │ don't copy image files to output directory │ │ │ │ │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ ├── ./usr/share/man/man1/mia-2dseriescorr.1.gz │ │ │ ├── mia-2dseriescorr.1 │ │ │ │ @@ -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=(required, input); io" │ │ │ │ +.IP "\-i \-\-in-base=(input, required); io" │ │ │ │ input file name base │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-o \-\-outname=(required, output); io" │ │ │ │ +.IP "\-o \-\-outname=(output, required); io" │ │ │ │ output file name to save the avarage per\-pixel correlation │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-z \-\-horizontal=(output); io" │ │ │ │ horiZontal correlation output file name │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-t \-\-vertical=(output); io" │ │ │ │ verTical correlation output file name │ │ ├── ./usr/share/man/man1/mia-2dseriesgradMAD.1.gz │ │ │ ├── mia-2dseriesgradMAD.1 │ │ │ │ @@ -8,15 +8,15 @@ │ │ │ │ .B mia\-2dseriesgradMAD │ │ │ │ Given a set of images of temporal succession, evaluates the pixel-wise temporal gradient and then its median average distance (MAD) and stores the result in an image. Spacial pre-filtering may be applied as given additional plugin(s) (filter/2dimage). │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-in-file=(input, required); string" │ │ │ │ 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 │ │ │ │ @@ -833,15 +833,15 @@ │ │ │ │ Intensity thresholding parameter: Pixels with intensities below this threshold will be set to zero, and also not used when evaluating mean and variation. │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ varfile │ │ │ │ -=(required, output, io) │ │ │ │ +=(output, required, io) │ │ │ │ .RS 2 │ │ │ │ name of the output file to save the variation image too.. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ @@ -869,15 +869,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B medianmad │ │ │ │ Filter that evaluates simultaniously the pixel wise median and the median absolute deviation (MAD) of an image in a given window. Pixel intensities below the given threshold will be ignored and at their loctions the output median and MAD are set to zero. The median intensity image is directly passed to the pipeline, the variation image is saved to a file given with the varfile parameter. Both output images have the same pixel type like the input image., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ madfile │ │ │ │ -=(required, output, io) │ │ │ │ +=(output, required, io) │ │ │ │ .RS 2 │ │ │ │ name of the output file to save the median absolute deviation image too.. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ @@ -1188,15 +1188,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B tee │ │ │ │ Save the input image to a file and also pass it through to the next filter, supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ file │ │ │ │ -=(required, output, io) │ │ │ │ +=(output, required, io) │ │ │ │ .RS 2 │ │ │ │ name of the output file to save the image too.. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ ├── ./usr/share/man/man1/mia-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=(input, required); string" │ │ │ │ input segmentation set │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ output file name │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-k \-\-skip=0" │ │ │ │ Skip files at the beginning │ │ │ │ │ │ │ │ .IP "\-e \-\-enlarge-boundary=5" │ │ │ │ Enlarge cropbox by number of pixels │ │ ├── ./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=(required, input); 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 │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dseriestovolume \-i \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dseriestovolume │ │ │ │ Obtaines a 3D volume image by combining the images of the segmentation set. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ input segmentation set │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(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-2dstack-cmeans-presegment.1.gz │ │ │ ├── mia-2dstack-cmeans-presegment.1 │ │ │ │ @@ -6,15 +6,15 @@ │ │ │ │ .B mia\-2dstack\-cmeans\-presegment \-i \-o \-L