--- /srv/rebuilderd/tmp/rebuilderdTlP1NV/inputs/mia-tools_2.4.7-16_amd64.deb +++ /srv/rebuilderd/tmp/rebuilderdTlP1NV/out/mia-tools_2.4.7-16_amd64.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 7572 2025-10-24 23:01:09.000000 control.tar.xz │ --rw-r--r-- 0 0 0 1997088 2025-10-24 23:01:09.000000 data.tar.xz │ +-rw-r--r-- 0 0 0 7588 2025-10-24 23:01:09.000000 control.tar.xz │ +-rw-r--r-- 0 0 0 1997256 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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│ +-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) 2130 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dstack-cmeans-presegment.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 6947 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dstackfilter.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1876 2025-10-24 23:01:09.000000 ./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) 1366 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dtrackpixelmovement.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1673 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) 1365 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) 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) 1634 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dbinarycombine.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1882 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) 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) 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) 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) 1879 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) 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) 6734 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) 1870 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) 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) 1670 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) 2318 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dfluid.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) 1673 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) 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) 1469 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dgetsize.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) 2201 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) 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) 5900 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) 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) 1548 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) 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) 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) 1267 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) 1299 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) 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) 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) 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) 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) 10019 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dprealign-nonrigid.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) 9539 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dnonrigidreg-alt.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) 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) 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) 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) 5112 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3drigidreg.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) 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) 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) 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) 1373 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dtrackpixelmovement.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1714 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dtransform.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) 1267 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dvectorfieldcreate.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) 1657 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) 1268 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) 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) 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) 1958 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) 882 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) 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) 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) 1959 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) 1656 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) 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) 1802 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-raw2volume.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 │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ .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" │ │ │ │ output mask image │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-p \-\-operation=nor" │ │ │ │ Operation to be applied │ │ ├── ./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-2dfluid-syn-registration.1.gz │ │ │ ├── mia-2dfluid-syn-registration.1 │ │ │ │ @@ -64,24 +64,24 @@ │ │ │ │ │ │ │ │ .IP " \-\-version" │ │ │ │ print the version number and exit │ │ │ │ │ │ │ │ .RE │ │ │ │ .SS IO │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-image=(required, input); io" │ │ │ │ +.IP "\-i \-\-in-image=(input, required); io" │ │ │ │ test image │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-r \-\-ref-image=(required, input); io" │ │ │ │ +.IP "\-r \-\-ref-image=(input, required); io" │ │ │ │ reference image │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-o \-\-transform=(required, output); io" │ │ │ │ +.IP "\-o \-\-transform=(output, required); io" │ │ │ │ output transformation │ │ │ │ For supported file types see PLUGINS:2dtransform/io │ │ │ │ -.IP "\-O \-\-inverse-transform=(required, output); io" │ │ │ │ +.IP "\-O \-\-inverse-transform=(output, required); io" │ │ │ │ inverse output transformation │ │ │ │ For supported file types see PLUGINS:2dtransform/io │ │ │ │ .RE │ │ │ │ .SS Processing │ │ │ │ .RS │ │ │ │ .IP " \-\-threads=\-1" │ │ │ │ Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (\-1: automatic estimation). │ │ ├── ./usr/share/man/man1/mia-2dgroundtruthreg.1.gz │ │ │ ├── mia-2dgroundtruthreg.1 │ │ │ │ @@ -15,15 +15,15 @@ │ │ │ │ .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" │ │ │ │ output perfusion data set │ │ │ │ │ │ │ │ .IP "\-r \-\-registered=reg" │ │ │ │ file name base for registered files │ │ ├── ./usr/share/man/man1/mia-2dimagecreator.1.gz │ │ │ ├── mia-2dimagecreator.1 │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dimagecreator \-o \-j [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dimagecreator │ │ │ │ This program is used to create test images. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ output file for create object │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-s \-\-size=[128,128]" │ │ │ │ size of the object │ │ │ │ │ │ │ │ .IP "\-r \-\-repn=ubyte" │ │ │ │ input pixel type │ │ ├── ./usr/share/man/man1/mia-2dimagefilter.1.gz │ │ │ ├── mia-2dimagefilter.1 │ │ │ │ @@ -7,15 +7,15 @@ │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dimagefilter │ │ │ │ This program runs a series filters on a given input image. The filters are given as extra parameters on the command line and Ware run in the order in which they are given. To obtain a list of available filters you may run │ │ │ │ 'mia-plugin-help filter/2dimage' │ │ │ │ from the command line │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ input image(s) to be filtered │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-o \-\-out-file=(required, output); io" │ │ │ │ output image(s) that have been filtered │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ │ │ @@ -348,15 +348,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B combiner │ │ │ │ Combine two images with the given combiner operator. if 'reverse' is set to false, the first operator is the image passed through the filter pipeline, and the second image is loaded from the file given with the 'image' parameter the moment the filter is run., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ image │ │ │ │ -=(required, input, io) │ │ │ │ +=(input, required, io) │ │ │ │ .RS 2 │ │ │ │ second image that is needed in the combiner. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ @@ -692,15 +692,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B labelmap │ │ │ │ Image filter to remap label id's. Only applicable to images with integer valued intensities/labels., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ map │ │ │ │ -=(required, input, string) │ │ │ │ +=(input, required, string) │ │ │ │ .RS 2 │ │ │ │ Label mapping file. │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ .B labelscale │ │ │ │ @@ -718,15 +718,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B load │ │ │ │ Load the input image from a file and use it to replace the current image in the pipeline., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ file │ │ │ │ -=(required, input, io) │ │ │ │ +=(input, required, io) │ │ │ │ .RS 2 │ │ │ │ name of the input file to load from.. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ @@ -757,15 +757,15 @@ │ │ │ │ .RE │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ input │ │ │ │ -=(required, input, io) │ │ │ │ +=(input, required, io) │ │ │ │ .RS 2 │ │ │ │ second input image file name. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ @@ -780,25 +780,25 @@ │ │ │ │ .TP 10 │ │ │ │ .B maxflow │ │ │ │ This filter implements the uses the max-flow min-cut algorithmfor image segmentation, supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ sink-flow │ │ │ │ -=(required, input, io) │ │ │ │ +=(input, required, io) │ │ │ │ .RS 2 │ │ │ │ Image of float type to define the per\-pixel flow to the sink. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ source-flow │ │ │ │ -=(required, input, io) │ │ │ │ +=(input, required, io) │ │ │ │ .RS 2 │ │ │ │ Image of float type to define the per\-pixel flow to the source. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ @@ -987,15 +987,15 @@ │ │ │ │ For supported plug-ins see PLUGINS:2dimage/shape │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ seed │ │ │ │ -=(required, input, io) │ │ │ │ +=(input, required, io) │ │ │ │ .RS 2 │ │ │ │ seed image (bit valued). │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ @@ -1168,15 +1168,15 @@ │ │ │ │ For supported plug-ins see PLUGINS:2dimage/shape │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ seed │ │ │ │ -=(required, input, string) │ │ │ │ +=(input, required, string) │ │ │ │ .RS 2 │ │ │ │ seed input image containing the labels for the initial regions. │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ .B tee │ │ │ │ @@ -1253,15 +1253,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B transform │ │ │ │ Transform the input image with the given transformation., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ file │ │ │ │ -=(required, input, io) │ │ │ │ +=(input, required, io) │ │ │ │ .RS 2 │ │ │ │ Name of the file containing the transformation.. │ │ │ │ For supported file types see PLUGINS:2dtransform/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ ├── ./usr/share/man/man1/mia-2dimagefilterstack.1.gz │ │ │ ├── mia-2dimagefilterstack.1 │ │ │ │ @@ -9,15 +9,15 @@ │ │ │ │ This program runs a series filters on a series of consecutive numbered input image. The filters are given as extra parameters on the command line and are run in the order in which they are given. │ │ │ │ .SH OPTIONS │ │ │ │ .SS File IO │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-in-file=(required, input); io" │ │ │ │ input image(s) to be filtered │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ output file name base, the file type is set accurding to the 'type' option │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-t \-\-type=" │ │ │ │ output file type, if not given the input type is used │ │ │ │ │ │ │ │ .RS 10 │ │ │ │ .I │ │ │ │ @@ -866,15 +866,15 @@ │ │ │ │ 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 │ │ │ │ @@ -902,15 +902,15 @@ │ │ │ │ .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 │ │ │ │ @@ -1221,15 +1221,15 @@ │ │ │ │ .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-2dimageregistration.1.gz │ │ │ ├── mia-2dimageregistration.1 │ │ │ │ @@ -6,18 +6,18 @@ │ │ │ │ .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" │ │ │ │ output transformation comprising the registration │ │ ├── ./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=(required, input); io" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ input images │ │ │ │ For supported file types see PLUGINS:2dimage/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 │ │ ├── ./usr/share/man/man1/mia-2dimagestack-cmeans.1.gz │ │ │ ├── mia-2dimagestack-cmeans.1 │ │ │ │ @@ -9,15 +9,15 @@ │ │ │ │ This program first evaluates a sparse histogram of an input image series, then runs a c-means classification over the histogram and then writes the probability mapping for thr original intensity values │ │ │ │ .SH OPTIONS │ │ │ │ .SS File-IO │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-in-file=(required, input); io" │ │ │ │ input image(s) to be filtered │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-o \-\-out-probmap=(required, output); string" │ │ │ │ +.IP "\-o \-\-out-probmap=(output, required); string" │ │ │ │ Save probability map to this file │ │ │ │ │ │ │ │ .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-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=(required, input); string" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ input perfusion data set │ │ │ │ │ │ │ │ .IP "\-o \-\-out-file=(required, output); 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=(output, required); io" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); 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-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=(required, input); string" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); 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-2dmyocard-segment.1.gz │ │ │ ├── mia-2dmyocard-segment.1 │ │ │ │ @@ -6,15 +6,15 @@ │ │ │ │ .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=(required, input); string" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ input perfusion data set │ │ │ │ │ │ │ │ .IP "\-o \-\-out-file=(output, required); 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 │ │ ├── ./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=(required, output); 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-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=(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 │ │ │ │ │ │ │ │ .IP " \-\-save-cropped=" │ │ │ │ save cropped set to this file │ │ ├── ./usr/share/man/man1/mia-2dmyoicapgt.1.gz │ │ │ ├── mia-2dmyoicapgt.1 │ │ │ │ @@ -43,15 +43,15 @@ │ │ │ │ │ │ │ │ .IP "\-T \-\-rho-thresh=0.85" │ │ │ │ correlation threshold for neighborhood analysis │ │ │ │ │ │ │ │ .RE │ │ │ │ .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=" │ │ │ │ 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-2dmyoperiodic-nonrigid.1.gz │ │ │ ├── mia-2dmyoperiodic-nonrigid.1 │ │ │ │ @@ -14,15 +14,15 @@ │ │ │ │ .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" │ │ │ │ output perfusion data set │ │ │ │ │ │ │ │ .IP "\-r \-\-registered=reg" │ │ │ │ file name base for registered fiels │ │ ├── ./usr/share/man/man1/mia-2dmyopgt-nonrigid.1.gz │ │ │ ├── mia-2dmyopgt-nonrigid.1 │ │ │ │ @@ -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=(output, required); string" │ │ │ │ +.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 │ │ │ │ │ │ │ │ .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=(input, required); string" │ │ │ │ +.IP "\-i \-\-input=(required, input); string" │ │ │ │ original segmentation set │ │ │ │ │ │ │ │ .IP "\-k \-\-skip=2" │ │ │ │ images to skip atthe bgin of the series │ │ │ │ │ │ │ │ .IP "\-r \-\-reference=20" │ │ │ │ reference image │ │ ├── ./usr/share/man/man1/mia-2dmyoset-all2one-nonrigid.1.gz │ │ │ ├── mia-2dmyoset-all2one-nonrigid.1 │ │ │ │ @@ -7,15 +7,15 @@ │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dmyoset\-all2one\-nonrigid │ │ │ │ This program runs non-rigid registration of a series of images given in an image set. All images are registered to one user defined reference image. │ │ │ │ .SH OPTIONS │ │ │ │ .SS │ │ │ │ File-IO │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ +.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ input perfusion data set │ │ │ │ │ │ │ │ .IP "\-o \-\-out-file=(output, required); string" │ │ │ │ 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. │ │ ├── ./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=(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 │ │ │ │ │ │ │ │ .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-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=(input, required); io" │ │ │ │ +.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ image to be segmented │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ +.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 │ │ │ │ │ │ │ │ .IP "\-b \-\-bias-correct" │ │ │ │ apply bias field correction │ │ ├── ./usr/share/man/man1/mia-2dsegment-fuzzyw.1.gz │ │ │ ├── mia-2dsegment-fuzzyw.1 │ │ │ │ @@ -6,15 +6,15 @@ │ │ │ │ .B mia\-2dsegment\-fuzzyw \-i [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dsegment\-fuzzyw │ │ │ │ This program is a implementation of a fuzzy c-means segmentation algorithm │ │ │ │ .SH OPTIONS │ │ │ │ .SS File I/O │ │ │ │ .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 "\-c \-\-cls-file=(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 "\-o \-\-out-file=(output); io" │ │ │ │ B\-field corrected image │ │ │ │ @@ -374,15 +374,15 @@ │ │ │ │ .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 │ │ │ │ @@ -718,15 +718,15 @@ │ │ │ │ .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 │ │ │ │ @@ -744,15 +744,15 @@ │ │ │ │ .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 │ │ │ │ @@ -783,15 +783,15 @@ │ │ │ │ .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 │ │ │ │ @@ -806,25 +806,25 @@ │ │ │ │ .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 │ │ │ │ @@ -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 │ │ │ │ -=(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 │ │ │ │ @@ -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 │ │ │ │ -=(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 │ │ │ │ @@ -1013,15 +1013,15 @@ │ │ │ │ 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 │ │ │ │ @@ -1194,28 +1194,28 @@ │ │ │ │ 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 │ │ │ │ -=(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 │ │ │ │ @@ -1279,15 +1279,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B transform │ │ │ │ Transform the input image with the given transformation., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ file │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ Name of the file containing the transformation.. │ │ │ │ For supported file types see PLUGINS:2dtransform/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ ├── ./usr/share/man/man1/mia-2dsegment-local-kmeans.1.gz │ │ │ ├── mia-2dsegment-local-kmeans.1 │ │ │ │ @@ -6,15 +6,15 @@ │ │ │ │ .B mia\-2dsegment\-local\-kmeans \-i [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dsegment\-local\-kmeans │ │ │ │ This program runs the segmentation of a 2D image by applying a localized k-means approach that helps to overcome intensity inhomogeneities in the image. The approach evaluates a global k-means clustering, and then separates the image into overlapping regions where more k-means iterations are run only including the locally present classes, i.e. the classes that relatively contain more pixels than a given threshold. │ │ │ │ .SH OPTIONS │ │ │ │ .SS File-IO │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ +.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ image to be segmented │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-o \-\-out-file=(output); io" │ │ │ │ class label image based on merging local labels │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-O \-\-out-file2=(output); io" │ │ │ │ class label image based on classifying by using the interpolated class centers │ │ ├── ./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=(required, output); 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-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 │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dsegshift \-i \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dsegshift │ │ │ │ This program move the segmentation(s) of an image series by using a shift that is equal for all slices. The program also may remove images from the begin of the series. The program can be used to correct the segmentation of the images if the images where cropped. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ input segmentation set │ │ │ │ For supported file types see PLUGINS:2dimage/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 │ │ ├── ./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=(input, required); string" │ │ │ │ +.IP "\-i \-\-in-set=(required, input); string" │ │ │ │ input segmentation set │ │ │ │ │ │ │ │ .IP "\-o \-\-out-set=(required, output); io" │ │ │ │ output image of minimal correlation │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-k \-\-skip=2" │ │ │ │ skip images at beginning of series │ │ ├── ./usr/share/man/man1/mia-2dseries-sectionmask.1.gz │ │ │ ├── mia-2dseries-sectionmask.1 │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ .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=(required, output); io" │ │ │ │ +.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 │ │ │ │ │ │ │ │ .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=(required, input); string" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); 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=(input, required); string" │ │ │ │ input segmentation set │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ output image name │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-k \-\-skip=0" │ │ │ │ Skip files at the beginning │ │ │ │ │ │ │ │ .IP "\-e \-\-enlarge-boundary=5" │ │ │ │ Enlarge cropbox by number of pixels │ │ │ │ @@ -842,15 +842,15 @@ │ │ │ │ Intensity thresholding parameter: Pixels with intensities below this threshold will be set to zero, and also not used when evaluating mean and variation. │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ varfile │ │ │ │ -=(required, output, io) │ │ │ │ +=(output, required, io) │ │ │ │ .RS 2 │ │ │ │ name of the output file to save the variation image too.. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ @@ -878,15 +878,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B medianmad │ │ │ │ Filter that evaluates simultaniously the pixel wise median and the median absolute deviation (MAD) of an image in a given window. Pixel intensities below the given threshold will be ignored and at their loctions the output median and MAD are set to zero. The median intensity image is directly passed to the pipeline, the variation image is saved to a file given with the varfile parameter. Both output images have the same pixel type like the input image., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ madfile │ │ │ │ -=(required, output, io) │ │ │ │ +=(output, required, io) │ │ │ │ .RS 2 │ │ │ │ name of the output file to save the median absolute deviation image too.. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ @@ -1197,15 +1197,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B tee │ │ │ │ Save the input image to a file and also pass it through to the next filter, supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ file │ │ │ │ -=(required, output, io) │ │ │ │ +=(output, required, io) │ │ │ │ .RS 2 │ │ │ │ name of the output file to save the image too.. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ ├── ./usr/share/man/man1/mia-2dseries2sets.1.gz │ │ │ ├── mia-2dseries2sets.1 │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dseries2sets \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dseries2sets │ │ │ │ This program takes all image files that are given as free parameters on the command line and creates segmentation sets based on information found in the images. Used information is the z-location of the slice and the acquisition number. The code is 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=(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 │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dseriesgradvariation \-i \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .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" │ │ │ │ +.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 │ │ ├── ./usr/share/man/man1/mia-2dseriessmoothgradMAD.1.gz │ │ │ ├── mia-2dseriessmoothgradMAD.1 │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dseriessmoothgradMAD \-i \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .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" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ input segmentation set │ │ │ │ │ │ │ │ .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 │ │ │ │ @@ -358,15 +358,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B combiner │ │ │ │ Combine two images with the given combiner operator. if 'reverse' is set to false, the first operator is the image passed through the filter pipeline, and the second image is loaded from the file given with the 'image' parameter the moment the filter is run., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ image │ │ │ │ -=(required, input, io) │ │ │ │ +=(input, required, io) │ │ │ │ .RS 2 │ │ │ │ second image that is needed in the combiner. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ @@ -702,15 +702,15 @@ │ │ │ │ .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 │ │ │ │ @@ -728,15 +728,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B load │ │ │ │ Load the input image from a file and use it to replace the current image in the pipeline., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ file │ │ │ │ -=(required, input, io) │ │ │ │ +=(input, required, io) │ │ │ │ .RS 2 │ │ │ │ name of the input file to load from.. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ @@ -767,15 +767,15 @@ │ │ │ │ .RE │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ input │ │ │ │ -=(required, input, io) │ │ │ │ +=(input, required, io) │ │ │ │ .RS 2 │ │ │ │ second input image file name. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ @@ -790,25 +790,25 @@ │ │ │ │ .TP 10 │ │ │ │ .B maxflow │ │ │ │ This filter implements the uses the max-flow min-cut algorithmfor image segmentation, supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ sink-flow │ │ │ │ -=(required, input, io) │ │ │ │ +=(input, required, io) │ │ │ │ .RS 2 │ │ │ │ Image of float type to define the per\-pixel flow to the sink. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ source-flow │ │ │ │ -=(required, input, io) │ │ │ │ +=(input, required, io) │ │ │ │ .RS 2 │ │ │ │ Image of float type to define the per\-pixel flow to the source. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ @@ -997,15 +997,15 @@ │ │ │ │ For supported plug-ins see PLUGINS:2dimage/shape │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ seed │ │ │ │ -=(required, input, io) │ │ │ │ +=(input, required, io) │ │ │ │ .RS 2 │ │ │ │ seed image (bit valued). │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ @@ -1178,15 +1178,15 @@ │ │ │ │ For supported plug-ins see PLUGINS:2dimage/shape │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ seed │ │ │ │ -=(required, input, string) │ │ │ │ +=(input, required, string) │ │ │ │ .RS 2 │ │ │ │ seed input image containing the labels for the initial regions. │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ .B tee │ │ │ │ @@ -1263,15 +1263,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B transform │ │ │ │ Transform the input image with the given transformation., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ file │ │ │ │ -=(required, input, io) │ │ │ │ +=(input, required, io) │ │ │ │ .RS 2 │ │ │ │ Name of the file containing the transformation.. │ │ │ │ For supported file types see PLUGINS:2dtransform/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ ├── ./usr/share/man/man1/mia-2dseriestovolume.1.gz │ │ │ ├── mia-2dseriestovolume.1 │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dseriestovolume \-i \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dseriestovolume │ │ │ │ Obtaines a 3D volume image by combining the images of the segmentation set. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ input segmentation set │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ output 3D image │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ .IP "\-k \-\-skip=0" │ │ │ │ number of frames to skip at the beginning of the series. │ │ │ │ │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ ├── ./usr/share/man/man1/mia-2dstack-cmeans-presegment.1.gz │ │ │ ├── mia-2dstack-cmeans-presegment.1 │ │ │ │ @@ -6,24 +6,24 @@ │ │ │ │ .B mia\-2dstack\-cmeans\-presegment \-i \-o \-L