--- /srv/rebuilderd/tmp/rebuilderdBuNSox/inputs/mia-tools_2.4.7-16_arm64.deb +++ /srv/rebuilderd/tmp/rebuilderdBuNSox/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 1791096 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 │ │ │ @@ -144,141 +144,141 @@ │ │ │ -rw-r--r-- 0 root (0) root (0) 1127 2025-10-24 23:01:09.000000 ./usr/share/doc/mia-tools/copyright │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-10-24 23:01:09.000000 ./usr/share/lintian/ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-10-24 23:01:09.000000 ./usr/share/lintian/overrides/ │ │ │ -rw-r--r-- 0 root (0) root (0) 186 2025-10-24 23:01:09.000000 ./usr/share/lintian/overrides/mia-tools │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-10-24 23:01:09.000000 ./usr/share/man/ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-10-24 23:01:09.000000 ./usr/share/man/man1/ │ │ │ -rw-r--r-- 0 root (0) root (0) 1472 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2davgmasked.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1566 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dbinarycombine.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1565 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dbinarycombine.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 2633 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2dcost.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1745 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2ddeform.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1696 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-2ddistance.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 1867 2025-10-24 23:01:09.000000 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./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) 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) 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) 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) 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) 6732 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dcost.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1645 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dcrispsegment.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1866 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3ddeform.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 2013 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3ddistance-stats.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1143 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3ddistance.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 1878 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3deval-transformquantity.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1673 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dfield2norm.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 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) 3574 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) 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) 1970 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) 5698 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) 1544 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) 1301 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) 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) 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) 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) 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) 2567 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-3dsegment-local-cmeans.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 9439 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) 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) 1120 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) 986 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) 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) 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) 2433 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-meshfilter.1.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1656 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-multihist.1.gz │ │ │ --rw-r--r-- 0 root (0) root (0) 901 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-myowavelettest.1.gz │ │ │ +-rw-r--r-- 0 root (0) root (0) 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) 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) 1086 2025-10-24 23:01:09.000000 ./usr/share/man/man1/mia-wavelettrans.1.gz │ │ ├── ./usr/share/man/man1/mia-2dbinarycombine.1.gz │ │ │ ├── mia-2dbinarycombine.1 │ │ │ │ @@ -5,21 +5,21 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dbinarycombine \-1 \-2 \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dbinarycombine │ │ │ │ This program is used to combine two binary images by some kind of operation. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-1 \-\-file1=(required, input); io" │ │ │ │ +.IP "\-1 \-\-file1=(input, required); io" │ │ │ │ input mask image 1 │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-2 \-\-file2=(required, input); io" │ │ │ │ +.IP "\-2 \-\-file2=(input, required); io" │ │ │ │ input mask image 2 │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ output mask image │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-p \-\-operation=nor" │ │ │ │ Operation to be applied │ │ │ │ │ │ │ │ .RS 10 │ │ │ │ .I │ │ ├── ./usr/share/man/man1/mia-2ddeform.1.gz │ │ │ ├── mia-2ddeform.1 │ │ │ │ @@ -5,21 +5,21 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2ddeform \-i \-o \-t [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .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" │ │ │ │ +.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ input image │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ transformed image │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-t \-\-transformation=(input, required); io" │ │ │ │ +.IP "\-t \-\-transformation=(required, input); io" │ │ │ │ transformation vector field │ │ │ │ For supported file types see PLUGINS:2dvf/io │ │ │ │ .IP "\-p \-\-interpolator=bspline:d=3" │ │ │ │ image interpolator kernel │ │ │ │ For supported plugins see PLUGINS:1d/splinekernel │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ ├── ./usr/share/man/man1/mia-2ddistance.1.gz │ │ │ ├── mia-2ddistance.1 │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ .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=(required, output); string" │ │ │ │ output file, '\-': write to stdout │ │ │ │ │ │ │ │ .IP "\-s \-\-scale=1" │ │ │ │ distance scaling factor │ │ ├── ./usr/share/man/man1/mia-2deval-transformquantity.1.gz │ │ │ ├── mia-2deval-transformquantity.1 │ │ │ │ @@ -27,15 +27,15 @@ │ │ │ │ .SH OPTIONS │ │ │ │ .SS │ │ │ │ File-IO │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-in-file=(required, input); string" │ │ │ │ input point set, if this parameter is given a sparse evaluation of the quantity will be done, otherwise the quantity is evaluated for each grid point of the transformation range. │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(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" │ │ │ │ transformation of which the quantity will be evaluated. │ │ │ │ For supported file types see PLUGINS:2dtransform/io │ │ │ │ .RE │ │ │ │ .SS │ │ ├── ./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=(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" │ │ │ │ +.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-2dforce.1.gz │ │ │ ├── mia-2dforce.1 │ │ │ │ @@ -11,15 +11,15 @@ │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-src-file=(required, input); io" │ │ │ │ input image │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-r \-\-ref-file=(required, input); io" │ │ │ │ reference image │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ output force norm image │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-c \-\-cost=(required); string" │ │ │ │ cost function to use │ │ │ │ │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ ├── ./usr/share/man/man1/mia-2dgrayimage-combine-to-rgb.1.gz │ │ │ ├── mia-2dgrayimage-combine-to-rgb.1 │ │ │ │ @@ -14,15 +14,15 @@ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-g \-\-green=(input); io" │ │ │ │ input image for green channel │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-r \-\-red=(input); io" │ │ │ │ input image for red channel │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ combined output image │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ │ │ .RS │ │ │ │ .IP "\-V \-\-verbose=warning" │ │ │ │ verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are: │ │ ├── ./usr/share/man/man1/mia-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-2dimagefilter.1.gz │ │ │ ├── mia-2dimagefilter.1 │ │ │ │ @@ -7,18 +7,18 @@ │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dimagefilter │ │ │ │ This program runs a series filters on a given input image. The filters are given as extra parameters on the command line and Ware run in the order in which they are given. To obtain a list of available filters you may run │ │ │ │ 'mia-plugin-help filter/2dimage' │ │ │ │ from the command line │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ +.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ input image(s) to be filtered │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ output image(s) that have been filtered │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ │ │ .RS │ │ │ │ .IP "\-V \-\-verbose=warning" │ │ │ │ verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are: │ │ │ │ @@ -348,15 +348,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B combiner │ │ │ │ Combine two images with the given combiner operator. if 'reverse' is set to false, the first operator is the image passed through the filter pipeline, and the second image is loaded from the file given with the 'image' parameter the moment the filter is run., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ image │ │ │ │ -=(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 │ │ │ │ @@ -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 │ │ │ │ -=(input, required, string) │ │ │ │ +=(required, input, 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 │ │ │ │ -=(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 │ │ │ │ @@ -757,15 +757,15 @@ │ │ │ │ .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 │ │ │ │ @@ -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 │ │ │ │ -=(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 │ │ │ │ @@ -826,15 +826,15 @@ │ │ │ │ Intensity thresholding parameter: Pixels with intensities below this threshold will be set to zero, and also not used when evaluating mean and variation. │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ varfile │ │ │ │ -=(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 │ │ │ │ @@ -862,15 +862,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B medianmad │ │ │ │ Filter that evaluates simultaniously the pixel wise median and the median absolute deviation (MAD) of an image in a given window. Pixel intensities below the given threshold will be ignored and at their loctions the output median and MAD are set to zero. The median intensity image is directly passed to the pipeline, the variation image is saved to a file given with the varfile parameter. Both output images have the same pixel type like the input image., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ madfile │ │ │ │ -=(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 │ │ │ │ @@ -987,15 +987,15 @@ │ │ │ │ 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 │ │ │ │ @@ -1168,28 +1168,28 @@ │ │ │ │ For supported plug-ins see PLUGINS:2dimage/shape │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ seed │ │ │ │ -=(input, required, string) │ │ │ │ +=(required, input, string) │ │ │ │ .RS 2 │ │ │ │ seed input image containing the labels for the initial regions. │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ .B tee │ │ │ │ Save the input image to a file and also pass it through to the next filter, supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ file │ │ │ │ -=(output, required, io) │ │ │ │ +=(required, output, io) │ │ │ │ .RS 2 │ │ │ │ name of the output file to save the image too.. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ @@ -1253,15 +1253,15 @@ │ │ │ │ .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-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-2dimagestack-cmeans.1.gz │ │ │ ├── mia-2dimagestack-cmeans.1 │ │ │ │ @@ -6,18 +6,18 @@ │ │ │ │ .B mia\-2dimagestack\-cmeans \-i \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dimagestack\-cmeans │ │ │ │ This program first evaluates a sparse histogram of an input image series, then runs a c-means classification over the histogram and then writes the probability mapping for thr original intensity values │ │ │ │ .SH OPTIONS │ │ │ │ .SS File-IO │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ +.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ input image(s) to be filtered │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-o \-\-out-probmap=(output, required); string" │ │ │ │ +.IP "\-o \-\-out-probmap=(required, output); 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-2dimagestats.1.gz │ │ │ ├── mia-2dimagestats.1 │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dimagestats \-i [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dimagestats │ │ │ │ This progranm is used to evaluate some statistics of an image. Output is Mean, Variation, Median, and Median Average Distance of the intensity values. The program allows one to set a lower threshold and to cut off a percentage of the high intensity pixels │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ +.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ input image to be analyzed │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-t \-\-thresh=10" │ │ │ │ intensity thresh to ignore │ │ │ │ │ │ │ │ .IP "\-g \-\-high-thresh=0.05" │ │ │ │ upper histogram percentage to ignore │ │ ├── ./usr/share/man/man1/mia-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-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=(required, output); io" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ output norm image │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ │ │ .RS │ │ │ │ .IP "\-V \-\-verbose=warning" │ │ │ │ verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are: │ │ ├── ./usr/share/man/man1/mia-2dmultiimageregistration.1.gz │ │ │ ├── mia-2dmultiimageregistration.1 │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dmultiimageregistration \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dmultiimageregistration │ │ │ │ This program runs a non-rigid registration based on the given cost criteria and a given transformation model. Other than mia-2dnonrigidreg it doesn't support specific command line parameters to provide the images. Instead the images are specified dirctly when defining the cost function. Hence, image registrations can be executed that optimize the aligmnet of more than one image pair at the same time. Note, however, that all input images must be of the same dimension (in pixels) │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-o \-\-out-transform=(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-2dmultiimageto3d.1.gz │ │ │ ├── mia-2dmultiimageto3d.1 │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dmultiimageto3d \-i \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dmultiimageto3d │ │ │ │ This program is used to convert a 2D multi-image file to a 3D image. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ input images │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ -.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ output image │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ │ │ .RS │ │ │ │ .IP "\-V \-\-verbose=warning" │ │ │ │ verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are: │ │ ├── ./usr/share/man/man1/mia-2dmultiimagevar.1.gz │ │ │ ├── mia-2dmultiimagevar.1 │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dmultiimagevar \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dmultiimagevar │ │ │ │ This program evaluates the pixel-wise accumulated intensity variation of a set of image given on the command line. If the input image files contain more then one image all images are used. All images must be of the same size. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ output image │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ │ │ .RS │ │ │ │ .IP "\-V \-\-verbose=warning" │ │ │ │ verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are: │ │ ├── ./usr/share/man/man1/mia-2dmyocard-ica.1.gz │ │ │ ├── mia-2dmyocard-ica.1 │ │ │ │ @@ -6,15 +6,15 @@ │ │ │ │ .B mia\-2dmyocard\-ica \-i [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dmyocard\-ica │ │ │ │ This program is used to run a ICA on a series of myocardial perfusion images to create sythetic references that can be used for motion correction by image registration. If the aim is to run a full motion compensation then it is better to create a segmentation set and use mia-2dmyoica-nonrigid. If the input data is given by means of a segmentation set, then on can also use mia-2dmyocard-icaseries. │ │ │ │ This program is essentially used to test different options on how to run the ICA forreference image creation. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-base=(required, input); io" │ │ │ │ +.IP "\-i \-\-in-base=(input, required); io" │ │ │ │ input file name ofolloing pattern nameXXXX.ext X=numbers │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP " \-\-coefs=" │ │ │ │ output mixing coefficients to this file │ │ │ │ │ │ │ │ .IP "\-o \-\-out-base=(output); string" │ │ │ │ output file name base │ │ ├── ./usr/share/man/man1/mia-2dmyocard-icaseries.1.gz │ │ │ ├── mia-2dmyocard-icaseries.1 │ │ │ │ @@ -6,15 +6,15 @@ │ │ │ │ .B mia\-2dmyocard\-icaseries \-i [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dmyocard\-icaseries │ │ │ │ This program is used to run a ICA on a series of myocardial perfusion images given in a segmentation set in order to create sythetic references that can be used for motion correction by image registration. If the aim is to run a full motion compensation then it is better run mia-2dmyoica-nonrigid, since this program is essentially the same without the registration bits. │ │ │ │ .SH OPTIONS │ │ │ │ .SS File-IO │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(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-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 │ │ │ │ @@ -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=(input, required); string" │ │ │ │ +.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ input perfusion data set │ │ │ │ │ │ │ │ .IP "\-o \-\-out-file=(required, output); string" │ │ │ │ output perfusion data set │ │ │ │ │ │ │ │ .IP "\-r \-\-registered=reg" │ │ │ │ File name base for the registered images. Image type and numbering scheme are taken from the input images as given in the input data set. │ │ ├── ./usr/share/man/man1/mia-2dmyoica-nonrigid.1.gz │ │ │ ├── mia-2dmyoica-nonrigid.1 │ │ │ │ @@ -16,15 +16,15 @@ │ │ │ │ │ │ │ │ .SH OPTIONS │ │ │ │ .SS File-IO │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-in-file=(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-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-2dmyoicapgt.1.gz │ │ │ ├── mia-2dmyoicapgt.1 │ │ │ │ @@ -46,15 +46,15 @@ │ │ │ │ │ │ │ │ .RE │ │ │ │ .SS File-IO │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-in-file=(required, input); string" │ │ │ │ input perfusion data set │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(required, output); string" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); string" │ │ │ │ output perfusion data set │ │ │ │ │ │ │ │ .IP "\-r \-\-registered=" │ │ │ │ File name base for the registered images. Image type and numbering scheme are taken from the input images as given in the input data set. │ │ │ │ │ │ │ │ .IP " \-\-save-cropped=(output); string" │ │ │ │ save cropped set to this file, the image files will use the stem of the name as file name base │ │ ├── ./usr/share/man/man1/mia-2dmyomilles.1.gz │ │ │ ├── mia-2dmyomilles.1 │ │ │ │ @@ -18,15 +18,15 @@ │ │ │ │ │ │ │ │ .SH OPTIONS │ │ │ │ .SS File-IO │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-in-file=(required, input); string" │ │ │ │ input perfusion data set │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(required, output); string" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); string" │ │ │ │ output perfusion data set │ │ │ │ │ │ │ │ .IP "\-r \-\-registered=" │ │ │ │ file name base for registered files │ │ │ │ │ │ │ │ .IP " \-\-save-references=" │ │ │ │ save synthetic reference images to this file base │ │ ├── ./usr/share/man/man1/mia-2dmyopgt-nonrigid.1.gz │ │ │ ├── mia-2dmyopgt-nonrigid.1 │ │ │ │ @@ -19,15 +19,15 @@ │ │ │ │ .SH OPTIONS │ │ │ │ .SS │ │ │ │ File-IO │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-in-file=(required, input); string" │ │ │ │ input perfusion data set │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(required, output); string" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); string" │ │ │ │ output perfusion data set │ │ │ │ │ │ │ │ .IP "\-r \-\-registered=reg" │ │ │ │ file name base for registered files, the image file type is the same as given in the input data set │ │ │ │ │ │ │ │ .RE │ │ │ │ .SS │ │ ├── ./usr/share/man/man1/mia-2dmyoset-all2one-nonrigid.1.gz │ │ │ ├── mia-2dmyoset-all2one-nonrigid.1 │ │ │ │ @@ -10,15 +10,15 @@ │ │ │ │ .SH OPTIONS │ │ │ │ .SS │ │ │ │ File-IO │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-in-file=(input, required); string" │ │ │ │ input perfusion data set │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(required, output); string" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); string" │ │ │ │ output perfusion data set │ │ │ │ │ │ │ │ .IP " \-\-out-filebase=reg" │ │ │ │ file name basae for registered files, file type is deducted from the image file type in the input data set. │ │ │ │ │ │ │ │ .RE │ │ │ │ .SS │ │ ├── ./usr/share/man/man1/mia-2dsegcompare.1.gz │ │ │ ├── mia-2dsegcompare.1 │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dsegcompare \-i \-r [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dsegcompare │ │ │ │ This program is used to evaluate the Hausdorff distance between each frame of a perfusion time series of the input set to the corresponding frame of the reference set and prints the result to stdout. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(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 │ │ │ │ @@ -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 │ │ │ │ @@ -1194,15 +1194,15 @@ │ │ │ │ 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 │ │ │ │ @@ -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-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-2dsegshift.1.gz │ │ │ ├── mia-2dsegshift.1 │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dsegshift \-i \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dsegshift │ │ │ │ This program move the segmentation(s) of an image series by using a shift that is equal for all slices. The program also may remove images from the begin of the series. The program can be used to correct the segmentation of the images if the images where cropped. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(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" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ input segmentation set │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-g \-\-image-file=crop" │ │ │ │ output image filename base │ │ │ │ │ │ │ │ .IP "\-S \-\-shift=[0,0]" │ │ │ │ shift of segmentation │ │ ├── ./usr/share/man/man1/mia-2dsegshiftperslice.1.gz │ │ │ ├── mia-2dsegshiftperslice.1 │ │ │ │ @@ -8,15 +8,15 @@ │ │ │ │ .B mia\-2dsegshiftperslice │ │ │ │ This program move the segmentation(s) of an image series by using a shift that is given on a per-slice base. The program can be used to correct the segmentation of the images if a linear registration was executed that only applies a translation and does not correct the segmentation automatically. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-in-file=(required, input); string" │ │ │ │ input segmentation set │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(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-sectionmask.1.gz │ │ │ ├── mia-2dseries-sectionmask.1 │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dseries\-sectionmask \-i \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dseries\-sectionmask │ │ │ │ Evaluate the masks for the sections of a segmented frame. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ input segmentation set │ │ │ │ │ │ │ │ .IP "\-o \-\-out-file=(required, output); io" │ │ │ │ output image containing the mask │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-f \-\-frame=0" │ │ │ │ Frame number for which to extract the mask │ │ ├── ./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-2dserieshausdorff.1.gz │ │ │ ├── mia-2dserieshausdorff.1 │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dserieshausdorff \-i \-r [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dserieshausdorff │ │ │ │ Get the per-slice Hausdorff distance of a segmentation with respect to a given reference segmentation set. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ input segmentation set │ │ │ │ │ │ │ │ -.IP "\-r \-\-ref-file=(required, input); string" │ │ │ │ +.IP "\-r \-\-ref-file=(input, required); string" │ │ │ │ reference segmentation set │ │ │ │ │ │ │ │ .IP "\-k \-\-skip=0" │ │ │ │ skip images at the beginning │ │ │ │ │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ ├── ./usr/share/man/man1/mia-2dseriessmoothgradMAD.1.gz │ │ │ ├── mia-2dseriessmoothgradMAD.1 │ │ │ │ @@ -8,15 +8,15 @@ │ │ │ │ .B mia\-2dseriessmoothgradMAD │ │ │ │ Given a set of images of temporal succession, evaluate the temporal pixel-wise gaussian and evaluate pixel-wise its MAD.A spacial pre-filtering may be applied by specifying additional plugins (filter/2dimage) │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-in-file=(input, required); string" │ │ │ │ input segmentation set │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ output file name │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-k \-\-skip=0" │ │ │ │ Skip files at the beginning │ │ │ │ │ │ │ │ .IP "\-e \-\-enlarge-boundary=5" │ │ │ │ Enlarge cropbox by number of pixels │ │ │ │ @@ -836,15 +836,15 @@ │ │ │ │ Intensity thresholding parameter: Pixels with intensities below this threshold will be set to zero, and also not used when evaluating mean and variation. │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ varfile │ │ │ │ -=(output, required, io) │ │ │ │ +=(required, output, io) │ │ │ │ .RS 2 │ │ │ │ name of the output file to save the variation image too.. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ @@ -872,15 +872,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B medianmad │ │ │ │ Filter that evaluates simultaniously the pixel wise median and the median absolute deviation (MAD) of an image in a given window. Pixel intensities below the given threshold will be ignored and at their loctions the output median and MAD are set to zero. The median intensity image is directly passed to the pipeline, the variation image is saved to a file given with the varfile parameter. Both output images have the same pixel type like the input image., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ madfile │ │ │ │ -=(output, required, io) │ │ │ │ +=(required, output, io) │ │ │ │ .RS 2 │ │ │ │ name of the output file to save the median absolute deviation image too.. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ @@ -1191,15 +1191,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B tee │ │ │ │ Save the input image to a file and also pass it through to the next filter, supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ file │ │ │ │ -=(output, required, io) │ │ │ │ +=(required, output, io) │ │ │ │ .RS 2 │ │ │ │ name of the output file to save the image too.. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ ├── ./usr/share/man/man1/mia-2dseriestovolume.1.gz │ │ │ ├── mia-2dseriestovolume.1 │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dseriestovolume \-i \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dseriestovolume │ │ │ │ Obtaines a 3D volume image by combining the images of the segmentation set. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ input segmentation set │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ output 3D image │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ .IP "\-k \-\-skip=0" │ │ │ │ number of frames to skip at the beginning of the series. │ │ │ │ │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ ├── ./usr/share/man/man1/mia-2dstackfilter.1.gz │ │ │ ├── mia-2dstackfilter.1 │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dstackfilter \-i \-o \-t [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dstackfilter │ │ │ │ This program is used to filter and convert a series of 2D gray scale images in a 3D fashion by running filters (filter/2dimage) as given on the command line. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ +.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ input image(s) to be filtered │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-o \-\-out-file=(output, required); io" │ │ │ │ output file name base, the actual names is created by adding the file number based on output order and the extension bysed on the 'type' parameter │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-t \-\-type=(required); set" │ │ │ │ output file type │ │ │ │ @@ -378,15 +378,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B combiner │ │ │ │ Combine two images with the given combiner operator. if 'reverse' is set to false, the first operator is the image passed through the filter pipeline, and the second image is loaded from the file given with the 'image' parameter the moment the filter is run., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ image │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ second image that is needed in the combiner. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ @@ -722,15 +722,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B labelmap │ │ │ │ Image filter to remap label id's. Only applicable to images with integer valued intensities/labels., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ map │ │ │ │ -=(input, required, string) │ │ │ │ +=(required, input, string) │ │ │ │ .RS 2 │ │ │ │ Label mapping file. │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ .B labelscale │ │ │ │ @@ -748,15 +748,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B load │ │ │ │ Load the input image from a file and use it to replace the current image in the pipeline., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ file │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ name of the input file to load from.. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ @@ -787,15 +787,15 @@ │ │ │ │ .RE │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ input │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ second input image file name. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ @@ -810,25 +810,25 @@ │ │ │ │ .TP 10 │ │ │ │ .B maxflow │ │ │ │ This filter implements the uses the max-flow min-cut algorithmfor image segmentation, supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ sink-flow │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ Image of float type to define the per\-pixel flow to the sink. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ source-flow │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ Image of float type to define the per\-pixel flow to the source. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ @@ -1017,15 +1017,15 @@ │ │ │ │ For supported plug-ins see PLUGINS:2dimage/shape │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ seed │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ seed image (bit valued). │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ @@ -1198,15 +1198,15 @@ │ │ │ │ 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 │ │ │ │ @@ -1283,15 +1283,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B transform │ │ │ │ Transform the input image with the given transformation., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ file │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ Name of the file containing the transformation.. │ │ │ │ For supported file types see PLUGINS:2dtransform/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ @@ -1625,15 +1625,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B label │ │ │ │ Stack Label filter, supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ map │ │ │ │ -=(input, required, string) │ │ │ │ +=(required, input, string) │ │ │ │ .RS 2 │ │ │ │ Mapfile to save label numbers that are joined. │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ @@ -1715,15 +1715,15 @@ │ │ │ │ low threshold for acceptance probability. │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ map │ │ │ │ -=(input, required, string) │ │ │ │ +=(required, input, string) │ │ │ │ .RS 2 │ │ │ │ seed class map. │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ ├── ./usr/share/man/man1/mia-2dto3dimage.1.gz │ │ │ ├── mia-2dto3dimage.1 │ │ │ │ @@ -8,15 +8,15 @@ │ │ │ │ .B mia\-2dto3dimage │ │ │ │ This program is used to combine a series of 2D images of equal size and type images following a certain numbering scheme to a 3D image. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-in-file=(input, required); io" │ │ │ │ input image(s) 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 file name │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ │ │ .RS │ │ │ │ .IP "\-V \-\-verbose=warning" │ │ │ │ verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are: │ │ ├── ./usr/share/man/man1/mia-2dto3dimageb.1.gz │ │ │ ├── mia-2dto3dimageb.1 │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-2dto3dimageb \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-2dto3dimageb │ │ │ │ This program is used to convert a series 2D images into a 3D image. The 2D images are read as additional command line parameters and the slice ordering corresponds to the ordering of the file names on the commend line. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ output file name │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ │ │ .RS │ │ │ │ .IP "\-V \-\-verbose=warning" │ │ │ │ verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are: │ │ ├── ./usr/share/man/man1/mia-2dtrackpixelmovement.1.gz │ │ │ ├── mia-2dtrackpixelmovement.1 │ │ │ │ @@ -10,21 +10,21 @@ │ │ │ │ id;time;x;y;z;reserved │ │ │ │ │ │ │ │ The fields 'time', 'x', 'y', and 'z' are updated, and the fields 'id' and 'reserved' are preserved, empty lines are ignored. │ │ │ │ .SH OPTIONS │ │ │ │ .SS │ │ │ │ File-IO │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ +.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ input point set │ │ │ │ │ │ │ │ .IP "\-o \-\-out-file=(required, output); string" │ │ │ │ output point set │ │ │ │ │ │ │ │ -.IP "\-t \-\-transformation=(input, required); io" │ │ │ │ +.IP "\-t \-\-transformation=(required, input); io" │ │ │ │ transformation describing the monitored change │ │ │ │ For supported file types see PLUGINS:2dtransform/io │ │ │ │ .RE │ │ │ │ .SS │ │ │ │ Parameters │ │ │ │ .RS │ │ │ │ .IP "\-T \-\-time-step=1" │ │ ├── ./usr/share/man/man1/mia-3dbinarycombine.1.gz │ │ │ ├── mia-3dbinarycombine.1 │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-3dbinarycombine \-1 \-2 \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-3dbinarycombine │ │ │ │ This program is used to combine two binary images by some kind of operation. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-1 \-\-file1=(required, input); io" │ │ │ │ +.IP "\-1 \-\-file1=(input, required); io" │ │ │ │ input mask image 1 │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ -.IP "\-2 \-\-file2=(required, input); io" │ │ │ │ +.IP "\-2 \-\-file2=(input, required); io" │ │ │ │ input mask image 2 │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ .IP "\-p \-\-operation=nor" │ │ │ │ Operation to be applied │ │ │ │ │ │ │ │ .RS 10 │ │ │ │ .I │ │ │ │ @@ -44,15 +44,15 @@ │ │ │ │ \(hy logocal xor │ │ │ │ .RE │ │ │ │ .RS 10 │ │ │ │ .I │ │ │ │ nxor │ │ │ │ \(hy logocal nxor │ │ │ │ .RE │ │ │ │ -.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ output mask image │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ │ │ .RS │ │ │ │ .IP "\-V \-\-verbose=warning" │ │ │ │ verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are: │ │ ├── ./usr/share/man/man1/mia-3dbrainextractT1.1.gz │ │ │ ├── mia-3dbrainextractT1.1 │ │ │ │ @@ -8,15 +8,15 @@ │ │ │ │ .B mia\-3dbrainextractT1 │ │ │ │ This program is used to extract the brain from T1 MR images. It first runs a combined fuzzy c-means clustering and B-field correction to facilitate a 3D segmentation of 3D image. Then various fiters are run to obtain a white matter segmentation as initial mask that is then used to run a region growing to obtain a mask of the whole brain. Finally, this mask is used to extact the brain from the B0 field corrected images. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-in-file=(input, required); io" │ │ │ │ input image(s) to be segmented │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ brain mask │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ .IP "\-n \-\-no-of-classes=3" │ │ │ │ number of classes │ │ │ │ │ │ │ │ .IP "\-w \-\-wm-class=2" │ │ │ │ index of white matter │ │ ├── ./usr/share/man/man1/mia-3dcombine-mr-segmentations.1.gz │ │ │ ├── mia-3dcombine-mr-segmentations.1 │ │ │ │ @@ -8,15 +8,15 @@ │ │ │ │ .B mia\-3dcombine\-mr\-segmentations │ │ │ │ This programs takes various segmentation masks of the same data and a tissue probability image set and combines them into one labeled image. The masks are translated to labels according to the position on the command line. If a voxel is set as belonging to more then one mask, the probabilities are consulted. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-in-file=(required, input); io" │ │ │ │ input probability images. The number of mask images must correspond to the number of probability images given here. │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ output image that contains the labeling. │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ │ │ .RS │ │ │ │ .IP "\-V \-\-verbose=warning" │ │ │ │ verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are: │ │ ├── ./usr/share/man/man1/mia-3dcost.1.gz │ │ │ ├── mia-3dcost.1 │ │ │ │ @@ -403,15 +403,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B combiner │ │ │ │ Combine two images with the given combiner operator. if 'reverse' is set to false, the first operator is the image passed through the filter pipeline, and the second image is loaded from the file given with the 'image' parameter the moment the filter is run., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ image │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ second image that is needed in the combiner. │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ @@ -717,15 +717,15 @@ │ │ │ │ lower threshold for mask growing. │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ ref │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ reference image for mask region growing. │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ @@ -798,15 +798,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B labelmap │ │ │ │ Image filter to remap label id's. Only applicable to images with integer valued intensities/labels., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ map │ │ │ │ -=(input, required, string) │ │ │ │ +=(required, input, string) │ │ │ │ .RS 2 │ │ │ │ Label mapping file. │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ .B labelscale │ │ │ │ @@ -824,15 +824,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B load │ │ │ │ Load the input image from a file and use it to replace the current image in the pipeline., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ file │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ name of the input file to load from.. │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ @@ -851,15 +851,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B mask │ │ │ │ Mask an image, one image is taken from the parameters list and the other from the normal filter input. Both images must be of the same dimensions and one must be binary. The attributes of the image coming through the filter pipeline are preserved. The output pixel type corresponds to the input image that is not binary., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ input │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ second input image file name. │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ @@ -1241,15 +1241,15 @@ │ │ │ │ For supported plug-ins see PLUGINS:3dimage/shape │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ seed │ │ │ │ -=(input, required, string) │ │ │ │ +=(required, input, string) │ │ │ │ .RS 2 │ │ │ │ seed input image containing the labels for the initial regions. │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ .B tee │ │ │ │ @@ -1275,15 +1275,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B transform │ │ │ │ Transform the input image with the given transformation., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ file │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ Name of the file containing the transformation.. │ │ │ │ For supported file types see PLUGINS:3dtransform/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ ├── ./usr/share/man/man1/mia-3dcrispsegment.1.gz │ │ │ ├── mia-3dcrispsegment.1 │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-3dcrispsegment \-i \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-3dcrispsegment │ │ │ │ This program creates a label image from a fuzzy segmentation. or each pixel the label is set to the class with the highest probability plus a given offset │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ input class file, should contain multiple images with tissue class probabilities │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ .IP "\-o \-\-out-file=(output, required); io" │ │ │ │ output class label image │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ .IP "\-l \-\-label-offset=1" │ │ │ │ label offset │ │ ├── ./usr/share/man/man1/mia-3ddeform.1.gz │ │ │ ├── mia-3ddeform.1 │ │ │ │ @@ -5,21 +5,21 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-3ddeform \-i \-o \-t [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-3ddeform │ │ │ │ Transform a 3D image by applying a given 3D transformation that is defined by a 3D vector field v according to x:=x-v(x) │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-image=(input, required); io" │ │ │ │ +.IP "\-i \-\-in-image=(required, input); io" │ │ │ │ input image │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ .IP "\-o \-\-out-image=(required, output); io" │ │ │ │ transformed image │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ -.IP "\-t \-\-transformation=(input, required); io" │ │ │ │ +.IP "\-t \-\-transformation=(required, input); io" │ │ │ │ transformation vector field │ │ │ │ For supported file types see PLUGINS:3dvf/io │ │ │ │ .IP "\-p \-\-interpolator=bspline:d=3" │ │ │ │ image interpolator kernel │ │ │ │ For supported plugins see PLUGINS:1d/splinekernel │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ ├── ./usr/share/man/man1/mia-3ddistance-stats.1.gz │ │ │ ├── mia-3ddistance-stats.1 │ │ │ │ @@ -33,15 +33,15 @@ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ .IP "\-r \-\-ref-labels=(required, input); io" │ │ │ │ reference label image │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ .IP "\-l \-\-label-map=(input); string" │ │ │ │ optional mapping of label numbers │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(required, output); string" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); string" │ │ │ │ output file name to write the distances to. The output file is a csv file, containing distances listed for each label. │ │ │ │ │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ │ │ .RS │ │ │ │ .IP "\-V \-\-verbose=warning" │ │ │ │ verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are: │ │ ├── ./usr/share/man/man1/mia-3ddistance.1.gz │ │ │ ├── mia-3ddistance.1 │ │ │ │ @@ -12,15 +12,15 @@ │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-in-file=(required, input); string" │ │ │ │ input image(s) that contain the source pixel mask │ │ │ │ │ │ │ │ .IP "\-r \-\-ref-file=(required, input); string" │ │ │ │ reference mask to evaluate the distance from │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(required, output); string" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); string" │ │ │ │ output file name │ │ │ │ │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ │ │ .RS │ │ │ │ .IP "\-V \-\-verbose=warning" │ │ │ │ verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are: │ │ ├── ./usr/share/man/man1/mia-3deval-transformquantity.1.gz │ │ │ ├── mia-3deval-transformquantity.1 │ │ │ │ @@ -27,15 +27,15 @@ │ │ │ │ .SH OPTIONS │ │ │ │ .SS │ │ │ │ File-IO │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-in-file=(input); string" │ │ │ │ input point set, if this parameter is given a sparse evaluation of the quantity will be done, otherwise the quantity is evaluated for each grid point of the transformation range. │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(output, required); string" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); string" │ │ │ │ output strains file, for a format description see above. │ │ │ │ │ │ │ │ .IP "\-t \-\-transformation=(input, required); io" │ │ │ │ transformation of which the quantity will be evaluated. │ │ │ │ For supported file types see PLUGINS:3dtransform/io │ │ │ │ .RE │ │ │ │ .SS │ │ ├── ./usr/share/man/man1/mia-3dfield2norm.1.gz │ │ │ ├── mia-3dfield2norm.1 │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-3dfield2norm \-i \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-3dfield2norm │ │ │ │ This program converts a 3d vector field to an image of its voxel-wise norm. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-vectorfield=(input, required); io" │ │ │ │ +.IP "\-i \-\-in-vectorfield=(required, input); io" │ │ │ │ input vector field │ │ │ │ For supported file types see PLUGINS:3dvf/io │ │ │ │ -.IP "\-o \-\-out-image=(required, output); io" │ │ │ │ +.IP "\-o \-\-out-image=(output, required); io" │ │ │ │ output image comprising the per voxel norm of each image │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ │ │ .RS │ │ │ │ .IP "\-V \-\-verbose=warning" │ │ │ │ verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are: │ │ ├── ./usr/share/man/man1/mia-3dfluid-syn-registration.1.gz │ │ │ ├── mia-3dfluid-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:3dimage/io │ │ │ │ -.IP "\-r \-\-ref-image=(required, input); io" │ │ │ │ +.IP "\-r \-\-ref-image=(input, required); io" │ │ │ │ reference image │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ -.IP "\-o \-\-transform=(output, required); io" │ │ │ │ +.IP "\-o \-\-transform=(required, output); io" │ │ │ │ output transformation │ │ │ │ For supported file types see PLUGINS:3dtransform/io │ │ │ │ -.IP "\-O \-\-inverse-transform=(output, required); io" │ │ │ │ +.IP "\-O \-\-inverse-transform=(required, output); io" │ │ │ │ inverse output transformation │ │ │ │ For supported file types see PLUGINS:3dtransform/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-3dfuzzysegment.1.gz │ │ │ ├── mia-3dfuzzysegment.1 │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-3dfuzzysegment \-i [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-3dfuzzysegment │ │ │ │ This program runs a combined fuzzy c-means clustering and B-field correction to facilitate a 3D segmentation of 3D image │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ +.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ input image(s) to be segmented │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ .IP "\-c \-\-cls-file=(output); io" │ │ │ │ output class probability images. Note, the used file format must support multiple images (best is to use vista) │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ .IP "\-o \-\-b0-file=(output); io" │ │ │ │ image corrected for intensity non\-uniformity │ │ ├── ./usr/share/man/man1/mia-3dgetsize.1.gz │ │ │ ├── mia-3dgetsize.1 │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-3dgetsize \-i [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-3dgetsize │ │ │ │ Write the dimensions of the input 3D image to stdout. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ input image(s) to be filtered │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ │ │ .RS │ │ │ │ .IP "\-V \-\-verbose=warning" │ │ │ │ verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are: │ │ ├── ./usr/share/man/man1/mia-3dgetslice.1.gz │ │ │ ├── mia-3dgetslice.1 │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-3dgetslice \-i \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-3dgetslice │ │ │ │ This program is used to extract 2D slices from a 3D data set and store them in separate files. Output files will be numbered according to their slice index. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ input image(s) to be filtered │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ -.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ output image(s). If number != 1 than this is used as a base name and should be given without extension since this will be based on the '\-\-type' option. If number=1 then this exact file name will be used. │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-t \-\-type=png" │ │ │ │ output file type for number != 1 │ │ │ │ │ │ │ │ .RS 10 │ │ │ │ .I │ │ ├── ./usr/share/man/man1/mia-3dimagecombine.1.gz │ │ │ ├── mia-3dimagecombine.1 │ │ │ │ @@ -5,24 +5,24 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-3dimagecombine \-1 \-2 \-c \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-3dimagecombine │ │ │ │ This program is used to combine two images using a given image combiner. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-1 \-\-image1=(input, required); io" │ │ │ │ +.IP "\-1 \-\-image1=(required, input); io" │ │ │ │ input image 1 to be combined │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ -.IP "\-2 \-\-image2=(input, required); io" │ │ │ │ +.IP "\-2 \-\-image2=(required, input); io" │ │ │ │ input image 2 to be combined │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ .IP "\-c \-\-combiner=(required); factory" │ │ │ │ combiner operation │ │ │ │ For supported plugins see PLUGINS:3dimage/combiner │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ output image file │ │ │ │ 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-3dimagefilter.1.gz │ │ │ ├── mia-3dimagefilter.1 │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-3dimagefilter \-i \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-3dimagefilter │ │ │ │ This program is used to filter and convert gray scale 3D images. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ +.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ input image(s) to be filtered │ │ │ │ For supported file types see PLUGINS:3dimage/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: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: │ │ │ │ @@ -264,15 +264,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B combiner │ │ │ │ Combine two images with the given combiner operator. if 'reverse' is set to false, the first operator is the image passed through the filter pipeline, and the second image is loaded from the file given with the 'image' parameter the moment the filter is run., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ image │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ second image that is needed in the combiner. │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ @@ -578,15 +578,15 @@ │ │ │ │ lower threshold for mask growing. │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ ref │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ reference image for mask region growing. │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ @@ -659,15 +659,15 @@ │ │ │ │ .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 │ │ │ │ @@ -685,15 +685,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B load │ │ │ │ Load the input image from a file and use it to replace the current image in the pipeline., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ file │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ name of the input file to load from.. │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ @@ -712,15 +712,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B mask │ │ │ │ Mask an image, one image is taken from the parameters list and the other from the normal filter input. Both images must be of the same dimensions and one must be binary. The attributes of the image coming through the filter pipeline are preserved. The output pixel type corresponds to the input image that is not binary., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ input │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ second input image file name. │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ @@ -1102,28 +1102,28 @@ │ │ │ │ For supported plug-ins see PLUGINS:3dimage/shape │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ seed │ │ │ │ -=(input, required, string) │ │ │ │ +=(required, input, string) │ │ │ │ .RS 2 │ │ │ │ seed input image containing the labels for the initial regions. │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ .B tee │ │ │ │ Save the input image to a file and also pass it through to the next filter, supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ file │ │ │ │ -=(required, output, io) │ │ │ │ +=(output, required, io) │ │ │ │ .RS 2 │ │ │ │ name of the output file to save the image too.. │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ @@ -1136,15 +1136,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B transform │ │ │ │ Transform the input image with the given transformation., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ file │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ Name of the file containing the transformation.. │ │ │ │ For supported file types see PLUGINS:3dtransform/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ ├── ./usr/share/man/man1/mia-3dimageselect.1.gz │ │ │ ├── mia-3dimageselect.1 │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-3dimageselect \-i \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-3dimageselect │ │ │ │ This program is used to select one 3D images from a multi-image file. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ +.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ input images │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ .IP "\-o \-\-out-file=(required, output); io" │ │ │ │ output image │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ .IP "\-n \-\-number=0" │ │ │ │ image number to be selected │ │ ├── ./usr/share/man/man1/mia-3dlandmarks-distances.1.gz │ │ │ ├── mia-3dlandmarks-distances.1 │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-3dlandmarks\-distances \-i \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-3dlandmarks\-distances │ │ │ │ Evaluate Euclidian distances between the corresponding landmarks in two landmark sets. The programs prints out only values for landmarks that are available and have location values in both sets │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file-1=(required, input); io" │ │ │ │ +.IP "\-i \-\-in-file-1=(input, required); io" │ │ │ │ input landmark set 1 │ │ │ │ For supported file types see PLUGINS:3dlandmarklist/io │ │ │ │ -.IP "\-o \-\-in-file-2=(required, input); io" │ │ │ │ +.IP "\-o \-\-in-file-2=(input, required); io" │ │ │ │ input landmark set 2 │ │ │ │ For supported file types see PLUGINS:3dlandmarklist/io │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ │ │ .RS │ │ │ │ .IP "\-V \-\-verbose=warning" │ │ │ │ verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are: │ │ ├── ./usr/share/man/man1/mia-3dlandmarks-transform.1.gz │ │ │ ├── mia-3dlandmarks-transform.1 │ │ │ │ @@ -5,21 +5,21 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-3dlandmarks\-transform \-i \-o \-t [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-3dlandmarks\-transform │ │ │ │ Transform the locations of the landmarks by means of a given 3D transformation. Note, landmark transformations do the inverse of an image transformation (in a manner of speaking), i.e. given a transformation V(x) in an image transformation the pixel intensity at x is set to the original intensity at V(x), while a landmark at x is moved to V(x). │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ input landmark set │ │ │ │ For supported file types see PLUGINS:3dlandmarklist/io │ │ │ │ .IP "\-o \-\-out-file=(required, output); io" │ │ │ │ output landmark set │ │ │ │ For supported file types see PLUGINS:3dlandmarklist/io │ │ │ │ -.IP "\-t \-\-transformation=(required, input); io" │ │ │ │ +.IP "\-t \-\-transformation=(input, required); io" │ │ │ │ transformation file │ │ │ │ For supported file types see PLUGINS:3dtransform/io │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ │ │ .RS │ │ │ │ .IP "\-V \-\-verbose=warning" │ │ │ │ verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are: │ │ ├── ./usr/share/man/man1/mia-3dlerp.1.gz │ │ │ ├── mia-3dlerp.1 │ │ │ │ @@ -5,21 +5,21 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-3dlerp \-1 \-2 \-o \-p [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-3dlerp │ │ │ │ merge two images by linear combination. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-1 \-\-first=(required, input); io" │ │ │ │ +.IP "\-1 \-\-first=(input, required); io" │ │ │ │ first input image │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ -.IP "\-2 \-\-second=(required, input); io" │ │ │ │ +.IP "\-2 \-\-second=(input, required); io" │ │ │ │ second input image │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ -.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ linearly interpolated image │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ .IP "\-p \-\-positions=(required); vfloat" │ │ │ │ image series positions (first, target, second) │ │ │ │ │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ ├── ./usr/share/man/man1/mia-3dmany2one-nonrigid.1.gz │ │ │ ├── mia-3dmany2one-nonrigid.1 │ │ │ │ @@ -7,15 +7,15 @@ │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-3dmany2one\-nonrigid │ │ │ │ This program runs the non-rigid registration of an image series by registereing all images to a user-selected reference. │ │ │ │ .SH OPTIONS │ │ │ │ .SS │ │ │ │ File-IO │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ input perfusion data set │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ .IP "\-o \-\-out-file=(output); io" │ │ │ │ file name for registered files │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ .RE │ │ │ │ .SS │ │ │ │ @@ -429,15 +429,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B combiner │ │ │ │ Combine two images with the given combiner operator. if 'reverse' is set to false, the first operator is the image passed through the filter pipeline, and the second image is loaded from the file given with the 'image' parameter the moment the filter is run., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ image │ │ │ │ -=(required, input, io) │ │ │ │ +=(input, required, io) │ │ │ │ .RS 2 │ │ │ │ second image that is needed in the combiner. │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ @@ -743,15 +743,15 @@ │ │ │ │ lower threshold for mask growing. │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ ref │ │ │ │ -=(required, input, io) │ │ │ │ +=(input, required, io) │ │ │ │ .RS 2 │ │ │ │ reference image for mask region growing. │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ @@ -824,15 +824,15 @@ │ │ │ │ .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 │ │ │ │ @@ -850,15 +850,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B load │ │ │ │ Load the input image from a file and use it to replace the current image in the pipeline., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ file │ │ │ │ -=(required, input, io) │ │ │ │ +=(input, required, io) │ │ │ │ .RS 2 │ │ │ │ name of the input file to load from.. │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ @@ -877,15 +877,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B mask │ │ │ │ Mask an image, one image is taken from the parameters list and the other from the normal filter input. Both images must be of the same dimensions and one must be binary. The attributes of the image coming through the filter pipeline are preserved. The output pixel type corresponds to the input image that is not binary., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ input │ │ │ │ -=(required, input, io) │ │ │ │ +=(input, required, io) │ │ │ │ .RS 2 │ │ │ │ second input image file name. │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ @@ -1267,28 +1267,28 @@ │ │ │ │ For supported plug-ins see PLUGINS:3dimage/shape │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ seed │ │ │ │ -=(required, input, string) │ │ │ │ +=(input, required, string) │ │ │ │ .RS 2 │ │ │ │ seed input image containing the labels for the initial regions. │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ .B tee │ │ │ │ Save the input image to a file and also pass it through to the next filter, supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ file │ │ │ │ -=(required, output, io) │ │ │ │ +=(output, required, io) │ │ │ │ .RS 2 │ │ │ │ name of the output file to save the image too.. │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ @@ -1301,15 +1301,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B transform │ │ │ │ Transform the input image with the given transformation., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ file │ │ │ │ -=(required, input, io) │ │ │ │ +=(input, required, io) │ │ │ │ .RS 2 │ │ │ │ Name of the file containing the transformation.. │ │ │ │ For supported file types see PLUGINS:3dtransform/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ ├── ./usr/share/man/man1/mia-3dmaskseeded.1.gz │ │ │ ├── mia-3dmaskseeded.1 │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-3dmaskseeded \-i \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-3dmaskseeded │ │ │ │ 3D image segmentation based on region growing from a seed point. Neighboring points are added, either when their intensity is equal or higher than that of the seed point, or of the intensity is lower or equal then that of the neighboring point. After region growing is finished, this mask is used to zero out the region in the original image yielding the resulting image. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ +.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ input image(s) to be filtered │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ output image(s) that have been filtered │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ .IP "\-s \-\-seed=[0,0,0]" │ │ │ │ seed point │ │ │ │ │ │ │ │ .IP "\-n \-\-neighborhood=6n" │ │ │ │ neighborhood shape │ │ ├── ./usr/share/man/man1/mia-3dmotioncompica-nonrigid.1.gz │ │ │ ├── mia-3dmotioncompica-nonrigid.1 │ │ │ │ @@ -14,15 +14,15 @@ │ │ │ │ .UE │ │ │ │ .RE │ │ │ │ │ │ │ │ . │ │ │ │ .SH OPTIONS │ │ │ │ .SS File-IO │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ input images of consecutively numbered filed (nameXXXX.ext) │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ .IP "\-o \-\-out-file=(output, required); io" │ │ │ │ output image name (as C format string including a %04d in order to define the file numbering) │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ .IP " \-\-save-refs=" │ │ │ │ save reference images, the given string is used as file name base, the number pattern follows the input images, and the output format is always 'vista' │ │ ├── ./usr/share/man/man1/mia-3dnonrigidreg.1.gz │ │ │ ├── mia-3dnonrigidreg.1 │ │ │ │ @@ -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:3dimage/io │ │ │ │ -.IP "\-r \-\-ref-image=(input, required); io" │ │ │ │ +.IP "\-r \-\-ref-image=(required, input); io" │ │ │ │ reference image │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ .IP "\-o \-\-out-image=(output, required); io" │ │ │ │ registered output image │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ .IP "\-t \-\-transformation=(output); io" │ │ │ │ output transformation │ │ │ │ @@ -430,15 +430,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B combiner │ │ │ │ Combine two images with the given combiner operator. if 'reverse' is set to false, the first operator is the image passed through the filter pipeline, and the second image is loaded from the file given with the 'image' parameter the moment the filter is run., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ image │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ second image that is needed in the combiner. │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ @@ -744,15 +744,15 @@ │ │ │ │ lower threshold for mask growing. │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ ref │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ reference image for mask region growing. │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ @@ -825,15 +825,15 @@ │ │ │ │ .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 │ │ │ │ @@ -851,15 +851,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B load │ │ │ │ Load the input image from a file and use it to replace the current image in the pipeline., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ file │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ name of the input file to load from.. │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ @@ -878,15 +878,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B mask │ │ │ │ Mask an image, one image is taken from the parameters list and the other from the normal filter input. Both images must be of the same dimensions and one must be binary. The attributes of the image coming through the filter pipeline are preserved. The output pixel type corresponds to the input image that is not binary., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ input │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ second input image file name. │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ @@ -1268,15 +1268,15 @@ │ │ │ │ For supported plug-ins see PLUGINS:3dimage/shape │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ seed │ │ │ │ -=(input, required, string) │ │ │ │ +=(required, input, string) │ │ │ │ .RS 2 │ │ │ │ seed input image containing the labels for the initial regions. │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ .B tee │ │ │ │ @@ -1302,15 +1302,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B transform │ │ │ │ Transform the input image with the given transformation., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ file │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ Name of the file containing the transformation.. │ │ │ │ For supported file types see PLUGINS:3dtransform/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ ├── ./usr/share/man/man1/mia-3dsegment-local-cmeans.1.gz │ │ │ ├── mia-3dsegment-local-cmeans.1 │ │ │ │ @@ -13,15 +13,15 @@ │ │ │ │ Dunmore CJ, Wollny G, Skinner MM. (2018) MIA-Clustering: a novel method for segmentation of paleontological material. PeerJ 6:e4374. │ │ │ │ .UE │ │ │ │ .RE │ │ │ │ │ │ │ │ .SH OPTIONS │ │ │ │ .SS File-IO │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ +.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ image to be segmented │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ .IP "\-o \-\-out-file=(output); io" │ │ │ │ class label image based on merging local labels │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ .IP "\-G \-\-out-global-crisp=(output); io" │ │ │ │ class label image based on global segmentation │ │ ├── ./usr/share/man/man1/mia-3dserial-nonrigid.1.gz │ │ │ ├── mia-3dserial-nonrigid.1 │ │ │ │ @@ -7,15 +7,15 @@ │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-3dserial\-nonrigid │ │ │ │ This program runs the image registration of a consecutively numbered image series. The registration is run in a serial manner, this is, only images in temporal succession (i.e. consecutive numbers) are registered, and the obtained transformations are applied accumulated to reach full registration. │ │ │ │ .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); string" │ │ │ │ file name for registered fiels │ │ │ │ │ │ │ │ .RE │ │ │ │ .SS │ │ │ │ @@ -429,15 +429,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B combiner │ │ │ │ Combine two images with the given combiner operator. if 'reverse' is set to false, the first operator is the image passed through the filter pipeline, and the second image is loaded from the file given with the 'image' parameter the moment the filter is run., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ image │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ second image that is needed in the combiner. │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ @@ -743,15 +743,15 @@ │ │ │ │ lower threshold for mask growing. │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ ref │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ reference image for mask region growing. │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ @@ -824,15 +824,15 @@ │ │ │ │ .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 │ │ │ │ @@ -850,15 +850,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B load │ │ │ │ Load the input image from a file and use it to replace the current image in the pipeline., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ file │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ name of the input file to load from.. │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ @@ -877,15 +877,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B mask │ │ │ │ Mask an image, one image is taken from the parameters list and the other from the normal filter input. Both images must be of the same dimensions and one must be binary. The attributes of the image coming through the filter pipeline are preserved. The output pixel type corresponds to the input image that is not binary., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ input │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ second input image file name. │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ @@ -1267,28 +1267,28 @@ │ │ │ │ For supported plug-ins see PLUGINS:3dimage/shape │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ seed │ │ │ │ -=(input, required, string) │ │ │ │ +=(required, input, string) │ │ │ │ .RS 2 │ │ │ │ seed input image containing the labels for the initial regions. │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ .B tee │ │ │ │ Save the input image to a file and also pass it through to the next filter, supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ file │ │ │ │ -=(required, output, io) │ │ │ │ +=(output, required, io) │ │ │ │ .RS 2 │ │ │ │ name of the output file to save the image too.. │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ │ │ @@ -1301,15 +1301,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B transform │ │ │ │ Transform the input image with the given transformation., supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ file │ │ │ │ -=(input, required, io) │ │ │ │ +=(required, input, io) │ │ │ │ .RS 2 │ │ │ │ Name of the file containing the transformation.. │ │ │ │ For supported file types see PLUGINS:3dtransform/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .RS 14 │ │ ├── ./usr/share/man/man1/mia-3dseries-track-intensity.1.gz │ │ │ ├── mia-3dseries-track-intensity.1 │ │ │ │ @@ -7,18 +7,18 @@ │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-3dseries\-track\-intensity │ │ │ │ This program tracks the intensity of a pixel at the given coordinates. │ │ │ │ .SH OPTIONS │ │ │ │ .SS │ │ │ │ File-IO │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ input perfusion data set │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ -.IP "\-o \-\-out-file=(required, output); string" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); string" │ │ │ │ file name for output intensity slopes │ │ │ │ │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ │ │ .RS │ │ │ │ .IP "\-V \-\-verbose=warning" │ │ │ │ verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are: │ │ ├── ./usr/share/man/man1/mia-3dtrackpixelmovement.1.gz │ │ │ ├── mia-3dtrackpixelmovement.1 │ │ │ │ @@ -10,21 +10,21 @@ │ │ │ │ id;time;x;y;z;reserved │ │ │ │ │ │ │ │ The fields 'time', 'x', 'y', and 'z' are updated, and the fields 'id' and 'reserved' are preserved, empty lines are ignored. │ │ │ │ .SH OPTIONS │ │ │ │ .SS │ │ │ │ File-IO │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ +.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ input point set │ │ │ │ │ │ │ │ .IP "\-o \-\-out-file=(output, required); string" │ │ │ │ output point set │ │ │ │ │ │ │ │ -.IP "\-t \-\-transformation=(input, required); io" │ │ │ │ +.IP "\-t \-\-transformation=(required, input); io" │ │ │ │ transformation describing the monitored change │ │ │ │ For supported file types see PLUGINS:3dtransform/io │ │ │ │ .RE │ │ │ │ .SS │ │ │ │ Parameters │ │ │ │ .RS │ │ │ │ .IP "\-T \-\-time-step=1" │ │ ├── ./usr/share/man/man1/mia-3dtransform.1.gz │ │ │ ├── mia-3dtransform.1 │ │ │ │ @@ -5,21 +5,21 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-3dtransform \-i \-o \-t [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-3dtransform │ │ │ │ Transform a 3D image by applying a given 3D transformation. │ │ │ │ .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:3dimage/io │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ transformed image │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ -.IP "\-t \-\-transformation=(input, required); io" │ │ │ │ +.IP "\-t \-\-transformation=(required, input); io" │ │ │ │ transformation file │ │ │ │ For supported file types see PLUGINS:3dtransform/io │ │ │ │ .IP "\-p \-\-interpolator=" │ │ │ │ override the interpolator provided by the transformation │ │ │ │ │ │ │ │ .IP "\-b \-\-boundary=mirror" │ │ │ │ override the boundary conditions provided by the transformation. This is only used if the interpolator is also overridden. │ │ ├── ./usr/share/man/man1/mia-3dvectorfieldcreate.1.gz │ │ │ ├── mia-3dvectorfieldcreate.1 │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-3dvectorfieldcreate \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-3dvectorfieldcreate │ │ │ │ This program is used to create a file containing a 3D vector field. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ output file for the vector field │ │ │ │ For supported file types see PLUGINS:3dvf/io │ │ │ │ .IP "\-s \-\-size=[64,64,64]" │ │ │ │ size of the vector field │ │ │ │ │ │ │ │ .IP "\-y \-\-ftype=0" │ │ │ │ vector field type │ │ ├── ./usr/share/man/man1/mia-3dvf2transform.1.gz │ │ │ ├── mia-3dvf2transform.1 │ │ │ │ @@ -8,15 +8,15 @@ │ │ │ │ .B mia\-3dvf2transform │ │ │ │ Creates a 3D transformation from a vector field. The input vector field is simply encapsulated into the transformation file format. The boundary conditions and the image interpolator kernel can be set at the command line. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-in-file=(input, required); io" │ │ │ │ input transformation │ │ │ │ For supported file types see PLUGINS:3dvf/io │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ output vector field │ │ │ │ For supported file types see PLUGINS:3dtransform/io │ │ │ │ .IP "\-k \-\-imgkernel=bspline:d=3" │ │ │ │ image interpolator kernel which is used when the transformation is applied to an image │ │ │ │ For supported plugins see PLUGINS:1d/splinekernel │ │ │ │ .IP "\-b \-\-imgboundary=mirror" │ │ │ │ Boundary condition applied when the transformation is used to transform an image │ │ ├── ./usr/share/man/man1/mia-cmeans.1.gz │ │ │ ├── mia-cmeans.1 │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-cmeans \-i \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-cmeans │ │ │ │ This Program reads a histogram from stdin and evaluates a cmeans classification of the intensity values into the given number of classes. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ input file name containing the histogram │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(required, output); string" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); string" │ │ │ │ output file name to store probabilities │ │ │ │ │ │ │ │ .IP "\-n \-\-nclasses=3" │ │ │ │ number of classes to partition into │ │ │ │ │ │ │ │ .IP "\-m \-\-max-iter=100" │ │ │ │ maximum number of iterations │ │ ├── ./usr/share/man/man1/mia-labelsort.1.gz │ │ │ ├── mia-labelsort.1 │ │ │ │ @@ -8,15 +8,15 @@ │ │ │ │ .B mia\-labelsort │ │ │ │ This program is used create a mapping based on a histogram that puts the intensities with high values at the beginning of the histogram. The main use case will be to sort labels of connected components in out-of-core image processing. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-in-file=(required, input); string" │ │ │ │ input file name containing the histogram │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(output, required); string" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); string" │ │ │ │ output file name to store probabilities │ │ │ │ │ │ │ │ .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-mesh-deformable-model.1.gz │ │ │ ├── mia-mesh-deformable-model.1 │ │ │ │ @@ -9,15 +9,15 @@ │ │ │ │ This program runs a deformable model to adapt a mesh to an iso-value within a given image. │ │ │ │ .SH OPTIONS │ │ │ │ .SS File I/O │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-in-file=(required, input); io" │ │ │ │ input mesh to be adapted │ │ │ │ For supported file types see PLUGINS:mesh/io │ │ │ │ -.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ output mesh that has been deformed │ │ │ │ For supported file types see PLUGINS:mesh/io │ │ │ │ .IP "\-r \-\-ref-file=(required, input); io" │ │ │ │ reference image │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ │ │ @@ -1152,15 +1152,15 @@ │ │ │ │ .TP 10 │ │ │ │ .B tee │ │ │ │ Save the input image to a file and also pass it through to the next filter, supported parameters are: │ │ │ │ .P │ │ │ │ .RS 14 │ │ │ │ .I │ │ │ │ file │ │ │ │ -=(required, output, io) │ │ │ │ +=(output, required, io) │ │ │ │ .RS 2 │ │ │ │ name of the output file to save the image too.. │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ .RE │ │ │ │ .RE │ │ │ │ .TP 10 │ │ ├── ./usr/share/man/man1/mia-mesh-to-maskimage.1.gz │ │ │ ├── mia-mesh-to-maskimage.1 │ │ │ │ @@ -6,18 +6,18 @@ │ │ │ │ .B mia\-mesh\-to\-maskimage \-i \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-mesh\-to\-maskimage │ │ │ │ This program converts a 3D mesh into a binary mask comprising the mesh surface. The output image size is either given on the command line or deducted from the mesh dimensions. │ │ │ │ .SH OPTIONS │ │ │ │ .SS File I/O │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ +.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ input mesh to be adapted │ │ │ │ For supported file types see PLUGINS:mesh/io │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ +.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ output image containing the binary mask │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ │ │ .RS │ │ │ │ .IP "\-V \-\-verbose=warning" │ │ │ │ verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are: │ │ ├── ./usr/share/man/man1/mia-meshdistance-to-stackmask.1.gz │ │ │ ├── mia-meshdistance-to-stackmask.1 │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-meshdistance\-to\-stackmask \-i \-r \-o [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-meshdistance\-to\-stackmask │ │ │ │ This program takes a binary masks and a triangular mesh as input and evaluates the distance of the mesh vertices to the binary maskand stores the result in a new mesh. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-mesh=(input, required); io" │ │ │ │ +.IP "\-i \-\-in-mesh=(required, input); io" │ │ │ │ input mesh │ │ │ │ For supported file types see PLUGINS:mesh/io │ │ │ │ -.IP "\-r \-\-ref-mask=(input, required); io" │ │ │ │ +.IP "\-r \-\-ref-mask=(required, input); io" │ │ │ │ reference binary mask │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ .IP "\-o \-\-out-mesh=(output, required); io" │ │ │ │ output mesh │ │ │ │ For supported file types see PLUGINS:mesh/io │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ ├── ./usr/share/man/man1/mia-myowavelettest.1.gz │ │ │ ├── mia-myowavelettest.1 │ │ │ │ @@ -6,15 +6,15 @@ │ │ │ │ .B mia\-myowavelettest \-i [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-myowavelettest │ │ │ │ This program runs the wavelet based slope-statistics on the mixing matrix of a ICA perfusion series. │ │ │ │ .SH OPTIONS │ │ │ │ .SS File-IO │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ input data set │ │ │ │ │ │ │ │ .RE │ │ │ │ .SS Help & Info │ │ │ │ .RS │ │ │ │ .IP "\-V \-\-verbose=warning" │ │ │ │ verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are: │ │ ├── ./usr/share/man/man1/mia-raw2image.1.gz │ │ │ ├── mia-raw2image.1 │ │ │ │ @@ -8,15 +8,15 @@ │ │ │ │ .B mia\-raw2image │ │ │ │ This program is used to convert raw data to a 2D file format. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ .IP "\-i \-\-in-file=(required, input); string" │ │ │ │ input file name │ │ │ │ │ │ │ │ -.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 "\-r \-\-repn=ubyte" │ │ │ │ input pixel type │ │ │ │ │ │ │ │ .RS 10 │ │ │ │ .I │ │ ├── ./usr/share/man/man1/mia-raw2volume.1.gz │ │ │ ├── mia-raw2volume.1 │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ .SH SYNOPSIS │ │ │ │ .B mia\-raw2volume \-i \-o \-s [options] │ │ │ │ .SH DESCRIPTION │ │ │ │ .B mia\-raw2volume │ │ │ │ This program is used to convert raw data into 3D images with appropriate metadata. │ │ │ │ .SH OPTIONS │ │ │ │ .RS │ │ │ │ -.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ +.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ input file name │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ output file name │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ .IP "\-r \-\-repn=ubyte" │ │ │ │ input pixel type │ │ │ │ │ │ │ │ .RS 10 │ │ │ │ .I