--- /srv/rebuilderd/tmp/rebuilderdu8IXeZ/inputs/mia-tools_2.4.7-16_arm64.deb +++ /srv/rebuilderd/tmp/rebuilderdu8IXeZ/out/mia-tools_2.4.7-16_arm64.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 1791280 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 1790908 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-3dcombine-mr-segmentations.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 3428 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dcost-translatedgrad.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 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) 6737 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dcost.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1650 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dcrispsegment.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) 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) 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) 2323 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dfluid.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) 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) 2200 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) 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) 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) 2199 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dgetslice.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1968 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dimageaddattributes.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1658 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dimagecombine.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1907 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dimagecreator.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 5701 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) 1548 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dimageselect.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) 5694 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dimagefilter.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 5895 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dimagefilterstack.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1543 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dimageselect.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1934 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dimagestatistics-in-mask.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1545 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) 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) 1296 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dlandmarks-transform.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 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) 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) 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) 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) 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) 2559 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dmotioncompica-nonrigid.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 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) 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) 5803 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dpropose-boundingbox.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) 5801 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dpropose-boundingbox.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 5110 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) 1935 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) 9444 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) 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) 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) 1710 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dtransform.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1313 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dtransform2vf.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1268 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dvectorfieldcreate.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1656 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) 1661 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) 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) 990 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) 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) 2433 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-meshfilter.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) 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) 2142 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-mesh-to-maskimage.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1955 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) 901 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-myowavelettest.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) 1740 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-raw2image.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1736 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-raw2image.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1802 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=(required, input); io" │ │ │ │ +.IP "\-1 \-\-file1=(input, required); io" │ │ │ │ input mask image 1 │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-2 \-\-file2=(required, input); io" │ │ │ │ +.IP "\-2 \-\-file2=(input, required); io" │ │ │ │ input mask image 2 │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-o \-\-out-file=(required, output); io" │ │ │ │ output mask image │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-p \-\-operation=nor" │ │ │ │ Operation to be applied │ │ ├── ./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=(output, required); io" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); 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=(input, required); io" │ │ │ │ input image │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-d \-\-distance-file=(input, required); io" │ │ │ │ distance field image (floating point) │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-o \-\-out-file=(required, output); string" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); 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" │ │ │ │ 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 │ │ │ │ @@ -64,18 +64,18 @@ │ │ │ │ │ │ │ │ .IP " \-\-version" │ │ │ │ print the version number and exit │ │ │ │ │ │ │ │ .RE │ │ │ │ .SS IO │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-image=(input, required); io" │ │ │ │ +.IP "\-i \-\-in-image=(required, input); io" │ │ │ │ test image │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-r \-\-ref-image=(input, required); io" │ │ │ │ +.IP "\-r \-\-ref-image=(required, input); io" │ │ │ │ reference image │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-o \-\-transform=(required, output); io" │ │ │ │ output transformation │ │ │ │ For supported file types see PLUGINS:2dtransform/io │ │ │ │ .IP "\-O \-\-inverse-transform=(required, output); io" │ │ │ │ inverse output transformation │ │ ├── ./usr/share/man/man1/mia-2dfluid.1.gz │ │ │ ├── mia-2dfluid.1 │ │ │ │ @@ -14,18 +14,18 @@ │ │ │ │ .UE │ │ │ │ .RE │ │ │ │ │ │ │ │ It uses SSD as the sole registration criterion. │ │ │ │ .SH OPTIONS │ │ │ │ .SS File-IO │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-image=(required, input); io" │ │ │ │ +.IP "\-i \-\-in-image=(input, required); io" │ │ │ │ input (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 │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-o \-\-out-transformation=(output); io" │ │ │ │ output transformation comprising the registration │ │ │ │ For supported file types see PLUGINS:2dvf/io │ │ │ │ .IP "\-d \-\-out-image=(output); io" │ │ │ │ output image deformed according to the transformation │ │ ├── ./usr/share/man/man1/mia-2dforce.1.gz │ │ │ ├── mia-2dforce.1 │ │ │ │ @@ -5,21 +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=(required, input); io" │ │ │ │ +.IP "\-i \-\-src-file=(input, required); io" │ │ │ │ input image │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-r \-\-ref-file=(required, input); io" │ │ │ │ +.IP "\-r \-\-ref-file=(input, required); 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-2dfuzzysegment.1.gz │ │ │ ├── mia-2dfuzzysegment.1 │ │ │ │ @@ -6,15 +6,15 @@ │ │ │ │ .B mia\-2dfuzzysegment \-i [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dfuzzysegment │ │ │ │ This program runs a combined fuzzy c-means clustering and B-field correction to facilitate a fuzzy segmentation of 2D image. cf D.L. Pham and J.L.Prince, "An adaptive fuzzy C-means algorithm for image segmentation in the presence of intensity inhomogeneities", Pat. Rec. Let., 20:57-68,1999 │ │ │ │ .SH OPTIONS │ │ │ │ .SS File-IO │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ input image(s) to be segmented │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-c \-\-cls-file=(output); io" │ │ │ │ output class probability images (floating point values and multi\-image) │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-o \-\-b0-file=(output); io" │ │ │ │ image corrected for intensity non\-uniformity │ │ ├── ./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=(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-2dimagefilterstack.1.gz │ │ │ ├── mia-2dimagefilterstack.1 │ │ │ │ @@ -6,15 +6,15 @@ │ │ │ │ .B mia\-2dimagefilterstack \-i \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dimagefilterstack │ │ │ │ This program runs a series filters on a series of consecutive numbered input image. The filters are given as extra parameters on the command line and are run in the order in which they are given. │ │ │ │ .SH OPTIONS │ │ │ │ .SS File IO │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ +.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ input image(s) to be filtered │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-o \-\-out-file=(output, required); io" │ │ │ │ output file name base, the file type is set accurding to the 'type' option │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-t \-\-type=" │ │ │ │ output file type, if not given the input type is used │ │ │ │ @@ -388,15 +388,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B combiner │ │ │ │ Combine two images with the given combiner operator. if 'reverse' is set to false, the first operator is the image passed through the filter pipeline, and the second image is loaded from the file given with the 'image' parameter the moment the filter is run., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ image │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ second image that is needed in the combiner. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ @@ -732,15 +732,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B labelmap │ │ │ │ Image filter to remap label id's. Only applicable to images with integer valued intensities/labels., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ map │ │ │ │ -=(input, required, string) │ │ │ │ +=(required, input, string) │ │ │ │ .RS 2 │ │ │ │ Label mapping file. │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ .B labelscale │ │ │ │ @@ -758,15 +758,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B load │ │ │ │ Load the input image from a file and use it to replace the current image in the pipeline., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ file │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ name of the input file to load from.. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ @@ -797,15 +797,15 @@ │ │ │ │ .RE │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ input │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ second input image file name. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ @@ -820,25 +820,25 @@ │ │ │ │ .TP 10 │ │ │ │ .B maxflow │ │ │ │ This filter implements the uses the max-flow min-cut algorithmfor image segmentation, supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ sink-flow │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ Image of float type to define the per\-pixel flow to the sink. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ source-flow │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ Image of float type to define the per\-pixel flow to the source. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ @@ -1027,15 +1027,15 @@ │ │ │ │ For supported plug-ins see PLUGINS:2dimage/shape │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ seed │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ seed image (bit valued). │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ @@ -1208,15 +1208,15 @@ │ │ │ │ For supported plug-ins see PLUGINS:2dimage/shape │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ seed │ │ │ │ -=(input, required, string) │ │ │ │ +=(required, input, string) │ │ │ │ .RS 2 │ │ │ │ seed input image containing the labels for the initial regions. │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ .B tee │ │ │ │ @@ -1293,15 +1293,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B transform │ │ │ │ Transform the input image with the given transformation., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ file │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ Name of the file containing the transformation.. │ │ │ │ For supported file types see PLUGINS:2dtransform/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ ├── ./usr/share/man/man1/mia-2dimagefullstats.1.gz │ │ │ ├── mia-2dimagefullstats.1 │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dimagefullstats \-i [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dimagefullstats │ │ │ │ This progranm is used to evaluate some statistics of an image. Output is Mean, Variation, Median, Min and Max of the intensity values. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ +.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ input image │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ │ │ .RS │ │ │ │ .IP "\-V \-\-verbose=warning" │ │ │ │ verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are: │ │ ├── ./usr/share/man/man1/mia-2dimageregistration.1.gz │ │ │ ├── mia-2dimageregistration.1 │ │ │ │ @@ -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=(input, required); io" │ │ │ │ +.IP "\-i \-\-in-image=(required, input); io" │ │ │ │ test image to be registered │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-r \-\-ref-image=(input, required); io" │ │ │ │ +.IP "\-r \-\-ref-image=(required, input); io" │ │ │ │ reference image 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=(output, required); io" │ │ │ │ +.IP "\-t \-\-transformation=(required, output); 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-2dlerp.1.gz │ │ │ ├── mia-2dlerp.1 │ │ │ │ @@ -5,21 +5,21 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dlerp \-1 \-2 \-o \-p [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dlerp │ │ │ │ Merge two images by pixel-wise linearly combining their intensities. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-1 \-\-first=(required, input); io" │ │ │ │ +.IP "\-1 \-\-first=(input, required); io" │ │ │ │ first input image │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-2 \-\-second=(required, input); io" │ │ │ │ +.IP "\-2 \-\-second=(input, required); io" │ │ │ │ second input image │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ output vector field │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-p \-\-positions=(required); vfloat" │ │ │ │ image series positions (first, target, second) │ │ │ │ │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ ├── ./usr/share/man/man1/mia-2dmany2one-nonrigid.1.gz │ │ │ ├── mia-2dmany2one-nonrigid.1 │ │ │ │ @@ -10,15 +10,15 @@ │ │ │ │ .SH OPTIONS │ │ │ │ .SS │ │ │ │ File-IO │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-in-file=(required, input); string" │ │ │ │ input perfusion data set │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(required, output); string" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); string" │ │ │ │ file name for registered images, numbering and pattern are deducted from the input data │ │ │ │ │ │ │ │ .RE │ │ │ │ .SS │ │ │ │ Registration │ │ │ │ .RS │ │ │ │ .IP "\-O \-\-optimizer=gsl:opt=gd,step=0.1" │ │ ├── ./usr/share/man/man1/mia-2dmultiimageregistration.1.gz │ │ │ ├── mia-2dmultiimageregistration.1 │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dmultiimageregistration \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dmultiimageregistration │ │ │ │ This program runs a non-rigid registration based on the given cost criteria and a given transformation model. Other than mia-2dnonrigidreg it doesn't support specific command line parameters to provide the images. Instead the images are specified dirctly when defining the cost function. Hence, image registrations can be executed that optimize the aligmnet of more than one image pair at the same time. Note, however, that all input images must be of the same dimension (in pixels) │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-o \-\-out-transform=(required, output); io" │ │ │ │ +.IP "\-o \-\-out-transform=(output, required); io" │ │ │ │ output transformation │ │ │ │ For supported file types see PLUGINS:2dtransform/io │ │ │ │ .IP "\-l \-\-levels=3" │ │ │ │ multi\-resolution levels │ │ │ │ │ │ │ │ .IP "\-O \-\-optimizer=gsl:opt=gd,step=0.1" │ │ │ │ Optimizer used for minimization │ │ ├── ./usr/share/man/man1/mia-2dmyocard-ica.1.gz │ │ │ ├── mia-2dmyocard-ica.1 │ │ │ │ @@ -6,15 +6,15 @@ │ │ │ │ .B mia\-2dmyocard\-ica \-i [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dmyocard\-ica │ │ │ │ This program is used to run a ICA on a series of myocardial perfusion images to create sythetic references that can be used for motion correction by image registration. If the aim is to run a full motion compensation then it is better to create a segmentation set and use mia-2dmyoica-nonrigid. If the input data is given by means of a segmentation set, then on can also use mia-2dmyocard-icaseries. │ │ │ │ This program is essentially used to test different options on how to run the ICA forreference image creation. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-base=(required, input); io" │ │ │ │ +.IP "\-i \-\-in-base=(input, required); io" │ │ │ │ input file name ofolloing pattern nameXXXX.ext X=numbers │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP " \-\-coefs=" │ │ │ │ output mixing coefficients to this file │ │ │ │ │ │ │ │ .IP "\-o \-\-out-base=(output); string" │ │ │ │ output file name base │ │ ├── ./usr/share/man/man1/mia-2dmyocard-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=(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 │ │ ├── ./usr/share/man/man1/mia-2dmyoica-full.1.gz │ │ │ ├── mia-2dmyoica-full.1 │ │ │ │ @@ -17,15 +17,15 @@ │ │ │ │ The software may first run a linear registration and then a non-linear registration or just one of the two.This version of the program can run all registrations in parallel. │ │ │ │ .SH OPTIONS │ │ │ │ .SS File-IO │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-in-file=(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=" │ │ │ │ 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-2dmyoica-nonrigid-parallel.1.gz │ │ │ ├── mia-2dmyoica-nonrigid-parallel.1 │ │ │ │ @@ -17,15 +17,15 @@ │ │ │ │ This version of the program runs all registrations in parallel. │ │ │ │ .SH OPTIONS │ │ │ │ .SS File-IO │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-in-file=(input, required); string" │ │ │ │ input perfusion data set │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(required, output); string" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); string" │ │ │ │ output perfusion data set │ │ │ │ │ │ │ │ .IP "\-r \-\-registered=reg" │ │ │ │ File name base for 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-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=(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-2dmyoica-nonrigid2.1.gz │ │ │ ├── mia-2dmyoica-nonrigid2.1 │ │ │ │ @@ -11,15 +11,15 @@ │ │ │ │ .SH OPTIONS │ │ │ │ .SS │ │ │ │ File-IO │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-in-file=(required, input); string" │ │ │ │ input perfusion data set │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(output, required); string" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); string" │ │ │ │ output perfusion data set │ │ │ │ │ │ │ │ .IP "\-r \-\-registered=reg" │ │ │ │ file name base for registered fiels │ │ │ │ │ │ │ │ .IP " \-\-save-cropped=" │ │ │ │ save cropped set to this file │ │ ├── ./usr/share/man/man1/mia-2dmyopgt-nonrigid.1.gz │ │ │ ├── mia-2dmyopgt-nonrigid.1 │ │ │ │ @@ -16,18 +16,18 @@ │ │ │ │ │ │ │ │ . │ │ │ │ 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=(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 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-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-2dsegment-ahmed.1.gz │ │ │ ├── mia-2dsegment-ahmed.1 │ │ │ │ @@ -16,15 +16,15 @@ │ │ │ │ │ │ │ │ changes are: p=2, and exp │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-in-file=(input, required); io" │ │ │ │ image to be segmented │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ +.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 │ │ │ │ @@ -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 │ │ │ │ @@ -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 │ │ │ │ -=(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-2dsegment-local-cmeans.1.gz │ │ │ ├── mia-2dsegment-local-cmeans.1 │ │ │ │ @@ -13,15 +13,15 @@ │ │ │ │ Dunmore CJ, Wollny G, Skinner MM. (2018) MIA-Clustering: a novel method for segmentation of paleontological material. PeerJ 6:e4374. │ │ │ │ .UE │ │ │ │ .RE │ │ │ │ │ │ │ │ .SH OPTIONS │ │ │ │ .SS File-IO │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ image to be segmented │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-o \-\-out-file=(output); io" │ │ │ │ class label image based on merging local labels │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-G \-\-out-global-crisp=(output); io" │ │ │ │ class label image based on global segmentation │ │ ├── ./usr/share/man/man1/mia-2dsegment-per-pixel-kmeans.1.gz │ │ │ ├── mia-2dsegment-per-pixel-kmeans.1 │ │ │ │ @@ -6,15 +6,15 @@ │ │ │ │ .B mia\-2dsegment\-per\-pixel\-kmeans \-i \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dsegment\-per\-pixel\-kmeans │ │ │ │ This program runs the segmentation of a 2D image by applying a localized k-means approach that helps to overcome intensity inhomogeneities in the image. The approach evaluates a global k-means clustering, and then separates the image into overlapping regions where more k-means iterations are run only including the locally present classes, i.e. the classes that relatively contain more pixels than a given threshold. │ │ │ │ .SH OPTIONS │ │ │ │ .SS File-IO │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ image to be segmented │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-o \-\-out-file=(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-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=(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-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=(output, required); io" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ output image name │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-k \-\-skip=0" │ │ │ │ Skip files at the beginning │ │ │ │ │ │ │ │ .IP "\-e \-\-enlarge-boundary=5" │ │ │ │ Enlarge cropbox by number of pixels │ │ │ │ @@ -842,15 +842,15 @@ │ │ │ │ Intensity thresholding parameter: Pixels with intensities below this threshold will be set to zero, and also not used when evaluating mean and variation. │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ varfile │ │ │ │ -=(output, required, io) │ │ │ │ +=(required, output, io) │ │ │ │ .RS 2 │ │ │ │ name of the output file to save the variation image too.. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ @@ -878,15 +878,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B medianmad │ │ │ │ Filter that evaluates simultaniously the pixel wise median and the median absolute deviation (MAD) of an image in a given window. Pixel intensities below the given threshold will be ignored and at their loctions the output median and MAD are set to zero. The median intensity image is directly passed to the pipeline, the variation image is saved to a file given with the varfile parameter. Both output images have the same pixel type like the input image., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ madfile │ │ │ │ -=(output, required, io) │ │ │ │ +=(required, output, io) │ │ │ │ .RS 2 │ │ │ │ name of the output file to save the median absolute deviation image too.. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ @@ -1197,15 +1197,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B tee │ │ │ │ Save the input image to a file and also pass it through to the next filter, supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ file │ │ │ │ -=(output, required, io) │ │ │ │ +=(required, output, io) │ │ │ │ .RS 2 │ │ │ │ name of the output file to save the image too.. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ ├── ./usr/share/man/man1/mia-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=(output, required); string" │ │ │ │ +.IP "\-o \-\-out-directory=(required, output); 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=(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-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=(input, required); string" │ │ │ │ +.IP "\-i \-\-in-file=(required, input); 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 │ │ │ │ -=(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 │ │ │ │ @@ -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 │ │ │ │ -=(input, required, string) │ │ │ │ +=(required, input, 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 │ │ │ │ -=(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 │ │ │ │ @@ -767,15 +767,15 @@ │ │ │ │ .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 │ │ │ │ @@ -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 │ │ │ │ -=(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 │ │ │ │ @@ -997,15 +997,15 @@ │ │ │ │ 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 │ │ │ │ @@ -1178,15 +1178,15 @@ │ │ │ │ For supported plug-ins see PLUGINS:2dimage/shape │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ seed │ │ │ │ -=(input, required, string) │ │ │ │ +=(required, input, string) │ │ │ │ .RS 2 │ │ │ │ seed input image containing the 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 │ │ │ │ -=(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-2dseriestovolume.1.gz │ │ │ ├── mia-2dseriestovolume.1 │ │ │ │ @@ -8,15 +8,15 @@ │ │ │ │ .B mia\-2dseriestovolume │ │ │ │ Obtaines a 3D volume image by combining the images of the segmentation set. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-in-file=(required, input); 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 │ │ │ │ @@ -6,24 +6,24 @@ │ │ │ │ .B mia\-2dstack\-cmeans\-presegment \-i \-o \-L