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0 root (0) root (0) 1881 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dbrainextractT1.1.gz\n -rw-r--r-- 0 root (0) root (0) 1740 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dcombine-imageseries.1.gz\n--rw-r--r-- 0 root (0) root (0) 1655 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dcombine-mr-segmentations.1.gz\n+-rw-r--r-- 0 root (0) root (0) 1650 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dcombine-mr-segmentations.1.gz\n -rw-r--r-- 0 root (0) root (0) 3428 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dcost-translatedgrad.1.gz\n--rw-r--r-- 0 root (0) root (0) 6734 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dcost.1.gz\n+-rw-r--r-- 0 root (0) root (0) 6736 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dcost.1.gz\n -rw-r--r-- 0 root (0) root (0) 1651 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dcrispsegment.1.gz\n--rw-r--r-- 0 root (0) root (0) 1869 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3ddeform.1.gz\n+-rw-r--r-- 0 root (0) root (0) 1866 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3ddeform.1.gz\n -rw-r--r-- 0 root (0) root (0) 2012 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3ddistance-stats.1.gz\n--rw-r--r-- 0 root (0) root (0) 1144 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3ddistance.1.gz\n+-rw-r--r-- 0 root (0) root (0) 1141 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3ddistance.1.gz\n -rw-r--r-- 0 root (0) root (0) 1875 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3deval-transformquantity.1.gz\n--rw-r--r-- 0 root (0) root (0) 1670 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dfield2norm.1.gz\n--rw-r--r-- 0 root (0) root (0) 3571 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dfluid-syn-registration.1.gz\n+-rw-r--r-- 0 root (0) root (0) 1673 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dfield2norm.1.gz\n+-rw-r--r-- 0 root (0) root (0) 3573 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dfluid-syn-registration.1.gz\n -rw-r--r-- 0 root (0) root (0) 2319 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dfluid.1.gz\n -rw-r--r-- 0 root (0) root (0) 2367 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dforce.1.gz\n--rw-r--r-- 0 root (0) root (0) 1708 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dfuzzysegment.1.gz\n--rw-r--r-- 0 root (0) root (0) 1468 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dgetsize.1.gz\n+-rw-r--r-- 0 root (0) root (0) 1706 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dfuzzysegment.1.gz\n+-rw-r--r-- 0 root (0) root (0) 1469 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dgetsize.1.gz\n -rw-r--r-- 0 root (0) root (0) 2203 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dgetslice.1.gz\n -rw-r--r-- 0 root (0) root (0) 1968 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dimageaddattributes.1.gz\n--rw-r--r-- 0 root (0) root (0) 1662 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dimagecombine.1.gz\n--rw-r--r-- 0 root (0) root (0) 1906 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dimagecreator.1.gz\n--rw-r--r-- 0 root (0) root (0) 5698 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dimagefilter.1.gz\n--rw-r--r-- 0 root (0) root (0) 5898 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dimagefilterstack.1.gz\n--rw-r--r-- 0 root (0) root (0) 1543 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dimageselect.1.gz\n+-rw-r--r-- 0 root (0) root (0) 1658 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dimagecombine.1.gz\n+-rw-r--r-- 0 root (0) root (0) 1907 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dimagecreator.1.gz\n+-rw-r--r-- 0 root (0) root (0) 5703 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dimagefilter.1.gz\n+-rw-r--r-- 0 root (0) root (0) 5902 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dimagefilterstack.1.gz\n+-rw-r--r-- 0 root (0) root (0) 1548 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dimageselect.1.gz\n -rw-r--r-- 0 root (0) root (0) 1934 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dimagestatistics-in-mask.1.gz\n -rw-r--r-- 0 root (0) root (0) 1545 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dimagestats.1.gz\n--rw-r--r-- 0 root (0) root (0) 1264 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3disosurface-from-stack.1.gz\n--rw-r--r-- 0 root (0) root (0) 2262 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3disosurface-from-volume.1.gz\n+-rw-r--r-- 0 root (0) root (0) 1267 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3disosurface-from-stack.1.gz\n+-rw-r--r-- 0 root (0) root (0) 2266 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3disosurface-from-volume.1.gz\n -rw-r--r-- 0 root (0) root (0) 1140 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dlandmarks-distances.1.gz\n -rw-r--r-- 0 root (0) root (0) 1299 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dlandmarks-transform.1.gz\n -rw-r--r-- 0 root (0) root (0) 1719 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dlerp.1.gz\n -rw-r--r-- 0 root (0) root (0) 7896 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dmany2one-nonrigid.1.gz\n--rw-r--r-- 0 root (0) root (0) 1878 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dmaskseeded.1.gz\n+-rw-r--r-- 0 root (0) root (0) 1877 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dmaskseeded.1.gz\n -rw-r--r-- 0 root (0) root (0) 2559 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dmotioncompica-nonrigid.1.gz\n--rw-r--r-- 0 root (0) root (0) 9545 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dnonrigidreg-alt.1.gz\n--rw-r--r-- 0 root (0) root (0) 9404 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dnonrigidreg.1.gz\n--rw-r--r-- 0 root (0) root (0) 10018 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dprealign-nonrigid.1.gz\n--rw-r--r-- 0 root (0) root (0) 5805 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dpropose-boundingbox.1.gz\n--rw-r--r-- 0 root (0) root (0) 5107 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3drigidreg.1.gz\n--rw-r--r-- 0 root (0) root (0) 1936 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dsegment-ahmed.1.gz\n+-rw-r--r-- 0 root (0) root (0) 9543 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dnonrigidreg-alt.1.gz\n+-rw-r--r-- 0 root (0) root (0) 9406 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dnonrigidreg.1.gz\n+-rw-r--r-- 0 root (0) root (0) 10024 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dprealign-nonrigid.1.gz\n+-rw-r--r-- 0 root (0) root (0) 5803 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dpropose-boundingbox.1.gz\n+-rw-r--r-- 0 root (0) root (0) 5112 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3drigidreg.1.gz\n+-rw-r--r-- 0 root (0) root (0) 1930 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dsegment-ahmed.1.gz\n -rw-r--r-- 0 root (0) root (0) 2568 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dsegment-local-cmeans.1.gz\n--rw-r--r-- 0 root (0) root (0) 9442 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dserial-nonrigid.1.gz\n--rw-r--r-- 0 root (0) root (0) 1590 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dseries-track-intensity.1.gz\n--rw-r--r-- 0 root (0) root (0) 1369 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dtrackpixelmovement.1.gz\n--rw-r--r-- 0 root (0) root (0) 1713 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dtransform.1.gz\n--rw-r--r-- 0 root (0) root (0) 1314 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dtransform2vf.1.gz\n--rw-r--r-- 0 root (0) root (0) 1267 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dvectorfieldcreate.1.gz\n+-rw-r--r-- 0 root (0) root (0) 9444 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dserial-nonrigid.1.gz\n+-rw-r--r-- 0 root (0) root (0) 1585 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dseries-track-intensity.1.gz\n+-rw-r--r-- 0 root (0) root (0) 1368 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dtrackpixelmovement.1.gz\n+-rw-r--r-- 0 root (0) root (0) 1718 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dtransform.1.gz\n+-rw-r--r-- 0 root (0) root (0) 1313 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dtransform2vf.1.gz\n+-rw-r--r-- 0 root (0) root (0) 1268 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dvectorfieldcreate.1.gz\n -rw-r--r-- 0 root (0) root (0) 1660 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dvf2transform.1.gz\n -rw-r--r-- 0 root (0) root (0) 1267 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-3dvfcompare.1.gz\n--rw-r--r-- 0 root (0) root (0) 1121 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-cmeans.1.gz\n--rw-r--r-- 0 root (0) root (0) 882 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-filenumberpattern.1.gz\n--rw-r--r-- 0 root (0) root (0) 991 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-labelsort.1.gz\n+-rw-r--r-- 0 root (0) root (0) 1120 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-cmeans.1.gz\n+-rw-r--r-- 0 root (0) root (0) 883 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-filenumberpattern.1.gz\n+-rw-r--r-- 0 root (0) root (0) 987 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-labelsort.1.gz\n -rw-r--r-- 0 root (0) root (0) 6458 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-mesh-deformable-model.1.gz\n--rw-r--r-- 0 root (0) root (0) 2139 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-mesh-to-maskimage.1.gz\n--rw-r--r-- 0 root (0) root (0) 1959 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-meshdistance-to-stackmask.1.gz\n--rw-r--r-- 0 root (0) root (0) 2433 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-meshfilter.1.gz\n+-rw-r--r-- 0 root (0) root (0) 2140 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-mesh-to-maskimage.1.gz\n+-rw-r--r-- 0 root (0) root (0) 1954 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-meshdistance-to-stackmask.1.gz\n+-rw-r--r-- 0 root (0) root (0) 2437 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-meshfilter.1.gz\n -rw-r--r-- 0 root (0) root (0) 1656 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-multihist.1.gz\n -rw-r--r-- 0 root (0) root (0) 900 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-myowavelettest.1.gz\n -rw-r--r-- 0 root (0) root (0) 850 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-plugin-help.1.gz\n--rw-r--r-- 0 root (0) root (0) 1740 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-raw2image.1.gz\n+-rw-r--r-- 0 root (0) root (0) 1741 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-raw2image.1.gz\n -rw-r--r-- 0 root (0) root (0) 1801 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-raw2volume.1.gz\n--rw-r--r-- 0 root (0) root (0) 1086 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-wavelettrans.1.gz\n+-rw-r--r-- 0 root (0) root (0) 1090 2023-08-29 09:00:00.000000 ./usr/share/man/man1/mia-wavelettrans.1.gz\n"}, {"source1": "./usr/share/man/man1/mia-2davgmasked.1.gz", "source2": "./usr/share/man/man1/mia-2davgmasked.1.gz", "unified_diff": null, "details": [{"source1": "mia-2davgmasked.1", "source2": "mia-2davgmasked.1", "unified_diff": "@@ -5,18 +5,18 @@\n .SH SYNOPSIS\n .B mia\\-2davgmasked \\-i \\-m [options]\n .SH DESCRIPTION\n .B mia\\-2davgmasked\n Evaluate average intensities of an image seriesThis program is used to evaluate the average intensity and its variation of a series of images in a given masked region.\n .SH OPTIONS\n .RS\n-.IP \"\\-i \\-\\-in-files=(input, required); io\"\n+.IP \"\\-i \\-\\-in-files=(required, input); io\"\n input image(s)\n For supported file types see PLUGINS:2dimage/io\n-.IP \"\\-m \\-\\-mask-file=(input, required); io\"\n+.IP \"\\-m \\-\\-mask-file=(required, input); io\"\n mask image, must be of type byte\n For supported file types see PLUGINS:2dimage/io\n .RE\n .SS Help & Info\n .RS\n .IP \"\\-V \\-\\-verbose=warning\"\n verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:\n"}]}, {"source1": "./usr/share/man/man1/mia-2dbinarycombine.1.gz", "source2": "./usr/share/man/man1/mia-2dbinarycombine.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dbinarycombine.1", "source2": "mia-2dbinarycombine.1", "unified_diff": "@@ -11,15 +11,15 @@\n .RS\n .IP \"\\-1 \\-\\-file1=(input, required); io\"\n input mask image 1\n For supported file types see PLUGINS:2dimage/io\n .IP \"\\-2 \\-\\-file2=(input, required); io\"\n input mask image 2\n For supported file types see PLUGINS:2dimage/io\n-.IP \"\\-o \\-\\-out-file=(required, output); io\"\n+.IP \"\\-o \\-\\-out-file=(output, required); io\"\n output mask image\n For supported file types see PLUGINS:2dimage/io\n .IP \"\\-p \\-\\-operation=nor\"\n Operation to be applied\n \n .RS 10\n .I\n"}]}, {"source1": "./usr/share/man/man1/mia-2ddeform.1.gz", "source2": "./usr/share/man/man1/mia-2ddeform.1.gz", "unified_diff": null, "details": [{"source1": "mia-2ddeform.1", "source2": "mia-2ddeform.1", "unified_diff": "@@ -5,21 +5,21 @@\n .SH SYNOPSIS\n .B mia\\-2ddeform \\-i \\-o \\-t [options]\n .SH DESCRIPTION\n .B mia\\-2ddeform\n 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)'\n .SH OPTIONS\n .RS\n-.IP \"\\-i \\-\\-in-file=(input, required); io\"\n+.IP \"\\-i \\-\\-in-file=(required, input); io\"\n input image\n For supported file types see PLUGINS:2dimage/io\n .IP \"\\-o \\-\\-out-file=(required, output); io\"\n transformed image\n For supported file types see PLUGINS:2dimage/io\n-.IP \"\\-t \\-\\-transformation=(input, required); io\"\n+.IP \"\\-t \\-\\-transformation=(required, input); io\"\n transformation vector field\n For supported file types see PLUGINS:2dvf/io\n .IP \"\\-p \\-\\-interpolator=bspline:d=3\"\n image interpolator kernel\n For supported plugins see PLUGINS:1d/splinekernel\n .RE\n .SS Help & Info\n"}]}, {"source1": "./usr/share/man/man1/mia-2ddistance.1.gz", "source2": "./usr/share/man/man1/mia-2ddistance.1.gz", "unified_diff": null, "details": [{"source1": "mia-2ddistance.1", "source2": "mia-2ddistance.1", "unified_diff": "@@ -11,15 +11,15 @@\n .RS\n .IP \"\\-i \\-\\-in-file=(required, input); io\"\n input image\n For supported file types see PLUGINS:2dimage/io\n .IP \"\\-d \\-\\-distance-file=(required, input); io\"\n distance field image (floating point)\n For supported file types see PLUGINS:2dimage/io\n-.IP \"\\-o \\-\\-out-file=(output, required); string\"\n+.IP \"\\-o \\-\\-out-file=(required, output); string\"\n output file, '\\-': write to stdout\n \n .IP \"\\-s \\-\\-scale=1\"\n distance scaling factor\n \n .IP \"\\-m \\-\\-method=avg\"\n distance measuring method\n"}]}, {"source1": "./usr/share/man/man1/mia-2dfluid-syn-registration.1.gz", "source2": "./usr/share/man/man1/mia-2dfluid-syn-registration.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dfluid-syn-registration.1", "source2": "mia-2dfluid-syn-registration.1", "unified_diff": "@@ -64,24 +64,24 @@\n \n .IP \" \\-\\-version\"\n print the version number and exit\n \n .RE\n .SS IO\n .RS\n-.IP \"\\-i \\-\\-in-image=(input, required); io\"\n+.IP \"\\-i \\-\\-in-image=(required, input); io\"\n test image\n For supported file types see PLUGINS:2dimage/io\n-.IP \"\\-r \\-\\-ref-image=(input, required); io\"\n+.IP \"\\-r \\-\\-ref-image=(required, input); io\"\n reference image\n For supported file types see PLUGINS:2dimage/io\n-.IP \"\\-o \\-\\-transform=(output, required); io\"\n+.IP \"\\-o \\-\\-transform=(required, output); io\"\n output transformation\n For supported file types see PLUGINS:2dtransform/io\n-.IP \"\\-O \\-\\-inverse-transform=(output, required); io\"\n+.IP \"\\-O \\-\\-inverse-transform=(required, output); io\"\n inverse output transformation\n For supported file types see PLUGINS:2dtransform/io\n .RE\n .SS Processing\n .RS\n .IP \" \\-\\-threads=\\-1\"\n 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).\n"}]}, {"source1": "./usr/share/man/man1/mia-2dforce.1.gz", "source2": "./usr/share/man/man1/mia-2dforce.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dforce.1", "source2": "mia-2dforce.1", "unified_diff": "@@ -5,21 +5,21 @@\n .SH SYNOPSIS\n .B mia\\-2dforce \\-i \\-r \\-o \\-c [options]\n .SH DESCRIPTION\n .B mia\\-2dforce\n This image evaluate the force field between two images based on a given cost function.\n .SH OPTIONS\n .RS\n-.IP \"\\-i \\-\\-src-file=(required, input); io\"\n+.IP \"\\-i \\-\\-src-file=(input, required); io\"\n input image\n For supported file types see PLUGINS:2dimage/io\n-.IP \"\\-r \\-\\-ref-file=(required, input); io\"\n+.IP \"\\-r \\-\\-ref-file=(input, required); io\"\n reference image\n For supported file types see PLUGINS:2dimage/io\n-.IP \"\\-o \\-\\-out-file=(output, required); io\"\n+.IP \"\\-o \\-\\-out-file=(required, output); io\"\n output force norm image\n For supported file types see PLUGINS:2dimage/io\n .IP \"\\-c \\-\\-cost=(required); string\"\n cost function to use\n \n .RE\n .SS Help & Info\n"}]}, {"source1": "./usr/share/man/man1/mia-2dgrayimage-combine-to-rgb.1.gz", "source2": "./usr/share/man/man1/mia-2dgrayimage-combine-to-rgb.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dgrayimage-combine-to-rgb.1", "source2": "mia-2dgrayimage-combine-to-rgb.1", "unified_diff": "@@ -14,15 +14,15 @@\n For supported file types see PLUGINS:2dimage/io\n .IP \"\\-g \\-\\-green=(input); io\"\n input image for green channel\n For supported file types see PLUGINS:2dimage/io\n .IP \"\\-r \\-\\-red=(input); io\"\n input image for red channel\n For supported file types see PLUGINS:2dimage/io\n-.IP \"\\-o \\-\\-out-file=(output, required); io\"\n+.IP \"\\-o \\-\\-out-file=(required, output); io\"\n combined output image\n For supported file types see PLUGINS:2dimage/io\n .RE\n .SS Help & Info\n .RS\n .IP \"\\-V \\-\\-verbose=warning\"\n verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:\n"}]}, {"source1": "./usr/share/man/man1/mia-2dgroundtruthreg.1.gz", "source2": "./usr/share/man/man1/mia-2dgroundtruthreg.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dgroundtruthreg.1", "source2": "mia-2dgroundtruthreg.1", "unified_diff": "@@ -18,15 +18,15 @@\n .SH OPTIONS\n .SS \n File-IO\n .RS\n .IP \"\\-i \\-\\-in-file=(required, input); string\"\n input perfusion data set\n \n-.IP \"\\-o \\-\\-out-file=(required, output); string\"\n+.IP \"\\-o \\-\\-out-file=(output, required); string\"\n output perfusion data set\n \n .IP \"\\-r \\-\\-registered=reg\"\n file name base for registered files\n \n .RE\n .SS \n"}]}, {"source1": "./usr/share/man/man1/mia-2dimagecombiner.1.gz", "source2": "./usr/share/man/man1/mia-2dimagecombiner.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dimagecombiner.1", "source2": "mia-2dimagecombiner.1", "unified_diff": "@@ -5,21 +5,21 @@\n .SH SYNOPSIS\n .B mia\\-2dimagecombiner \\-1 \\-2 \\-o [options]\n .SH DESCRIPTION\n .B mia\\-2dimagecombiner\n Combine two image by a given operation.\n .SH OPTIONS\n .RS\n-.IP \"\\-1 \\-\\-in-file-1=(required, input); io\"\n+.IP \"\\-1 \\-\\-in-file-1=(input, required); io\"\n first input image to be combined\n For supported file types see PLUGINS:2dimage/io\n-.IP \"\\-2 \\-\\-in-file-2=(required, input); io\"\n+.IP \"\\-2 \\-\\-in-file-2=(input, required); io\"\n second input image to be combined\n For supported file types see PLUGINS:2dimage/io\n-.IP \"\\-o \\-\\-out-file=(required, output); io\"\n+.IP \"\\-o \\-\\-out-file=(output, required); io\"\n output image(s) that have been filtered\n For supported file types see PLUGINS:2dimage/io\n .IP \"\\-p \\-\\-operation=absdiff\"\n operation to be applied\n For supported plugins see PLUGINS:2dimage/combiner\n .RE\n .SS Help & Info\n"}]}, {"source1": "./usr/share/man/man1/mia-2dimagecreator.1.gz", "source2": "./usr/share/man/man1/mia-2dimagecreator.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dimagecreator.1", "source2": "mia-2dimagecreator.1", "unified_diff": "@@ -5,15 +5,15 @@\n .SH SYNOPSIS\n .B mia\\-2dimagecreator \\-o \\-j [options]\n .SH DESCRIPTION\n .B mia\\-2dimagecreator\n This program is used to create test images.\n .SH OPTIONS\n .RS\n-.IP \"\\-o \\-\\-out-file=(output, required); io\"\n+.IP \"\\-o \\-\\-out-file=(required, output); io\"\n output file for create object\n For supported file types see PLUGINS:2dimage/io\n .IP \"\\-s \\-\\-size=[128,128]\"\n size of the object\n \n .IP \"\\-r \\-\\-repn=ubyte\"\n input pixel type \n"}]}, {"source1": "./usr/share/man/man1/mia-2dimagefilter.1.gz", "source2": "./usr/share/man/man1/mia-2dimagefilter.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dimagefilter.1", "source2": "mia-2dimagefilter.1", "unified_diff": "@@ -10,15 +10,15 @@\n 'mia-plugin-help filter/2dimage'\n from the command line\n .SH OPTIONS\n .RS\n .IP \"\\-i \\-\\-in-file=(required, input); io\"\n input image(s) to be filtered\n For supported file types see PLUGINS:2dimage/io\n-.IP \"\\-o \\-\\-out-file=(required, output); io\"\n+.IP \"\\-o \\-\\-out-file=(output, required); io\"\n output image(s) that have been filtered\n For supported file types see PLUGINS:2dimage/io\n .RE\n .SS Help & Info\n .RS\n .IP \"\\-V \\-\\-verbose=warning\"\n verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:\n@@ -826,15 +826,15 @@\n Intensity thresholding parameter: Pixels with intensities below this threshold will be set to zero, and also not used when evaluating mean and variation.\n \n .RE\n .RE\n .RS 14\n .I\n varfile\n-=(required, output, io)\n+=(output, required, io)\n .RS 2\n name of the output file to save the variation image too..\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .RS 14\n@@ -862,15 +862,15 @@\n .TP 10\n .B medianmad\n 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: \n .P\n .RS 14\n .I\n madfile\n-=(required, output, io)\n+=(output, required, io)\n .RS 2\n name of the output file to save the median absolute deviation image too..\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .RS 14\n@@ -1181,15 +1181,15 @@\n .TP 10\n .B tee\n Save the input image to a file and also pass it through to the next filter, supported parameters are: \n .P\n .RS 14\n .I\n file\n-=(required, output, io)\n+=(output, required, io)\n .RS 2\n name of the output file to save the image too..\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .TP 10\n"}]}, {"source1": "./usr/share/man/man1/mia-2dimagefilterstack.1.gz", "source2": "./usr/share/man/man1/mia-2dimagefilterstack.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dimagefilterstack.1", "source2": "mia-2dimagefilterstack.1", "unified_diff": "@@ -6,18 +6,18 @@\n .B mia\\-2dimagefilterstack \\-i \\-o [options] \n .SH DESCRIPTION\n .B mia\\-2dimagefilterstack\n 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.\n .SH OPTIONS\n .SS File IO\n .RS\n-.IP \"\\-i \\-\\-in-file=(input, required); io\"\n+.IP \"\\-i \\-\\-in-file=(required, input); io\"\n input image(s) to be filtered\n For supported file types see PLUGINS:2dimage/io\n-.IP \"\\-o \\-\\-out-file=(output, required); io\"\n+.IP \"\\-o \\-\\-out-file=(required, output); io\"\n output file name base, the file type is set accurding to the 'type' option\n For supported file types see PLUGINS:2dimage/io\n .IP \"\\-t \\-\\-type=\"\n output file type, if not given the input type is used\n \n .RS 10\n .I\n@@ -388,15 +388,15 @@\n .TP 10\n .B combiner\n 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: \n .P\n .RS 14\n .I\n image\n-=(input, required, io)\n+=(required, input, io)\n .RS 2\n second image that is needed in the combiner.\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .RS 14\n@@ -732,15 +732,15 @@\n .TP 10\n .B labelmap\n Image filter to remap label id's. Only applicable to images with integer valued intensities/labels., supported parameters are: \n .P\n .RS 14\n .I\n map\n-=(input, required, string)\n+=(required, input, string)\n .RS 2\n Label mapping file.\n \n .RE\n .RE\n .TP 10\n .B labelscale\n@@ -758,15 +758,15 @@\n .TP 10\n .B load\n Load the input image from a file and use it to replace the current image in the pipeline., supported parameters are: \n .P\n .RS 14\n .I\n file\n-=(input, required, io)\n+=(required, input, io)\n .RS 2\n name of the input file to load from..\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .TP 10\n@@ -797,15 +797,15 @@\n .RE\n \n .RE\n .RE\n .RS 14\n .I\n input\n-=(input, required, io)\n+=(required, input, io)\n .RS 2\n second input image file name.\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .RS 14\n@@ -820,25 +820,25 @@\n .TP 10\n .B maxflow\n This filter implements the uses the max-flow min-cut algorithmfor image segmentation, supported parameters are: \n .P\n .RS 14\n .I\n sink-flow\n-=(input, required, io)\n+=(required, input, io)\n .RS 2\n Image of float type to define the per\\-pixel flow to the sink.\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .RS 14\n .I\n source-flow\n-=(input, required, io)\n+=(required, input, io)\n .RS 2\n Image of float type to define the per\\-pixel flow to the source.\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .TP 10\n@@ -866,15 +866,15 @@\n Intensity thresholding parameter: Pixels with intensities below this threshold will be set to zero, and also not used when evaluating mean and variation.\n \n .RE\n .RE\n .RS 14\n .I\n varfile\n-=(output, required, io)\n+=(required, output, io)\n .RS 2\n name of the output file to save the variation image too..\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .RS 14\n@@ -902,15 +902,15 @@\n .TP 10\n .B medianmad\n 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: \n .P\n .RS 14\n .I\n madfile\n-=(output, required, io)\n+=(required, output, io)\n .RS 2\n name of the output file to save the median absolute deviation image too..\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .RS 14\n@@ -1027,15 +1027,15 @@\n For supported plug-ins see PLUGINS:2dimage/shape\n \n .RE\n .RE\n .RS 14\n .I\n seed\n-=(input, required, io)\n+=(required, input, io)\n .RS 2\n seed image (bit valued).\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .TP 10\n@@ -1208,28 +1208,28 @@\n For supported plug-ins see PLUGINS:2dimage/shape\n \n .RE\n .RE\n .RS 14\n .I\n seed\n-=(input, required, string)\n+=(required, input, string)\n .RS 2\n seed input image containing the lables for the initial regions.\n \n .RE\n .RE\n .TP 10\n .B tee\n Save the input image to a file and also pass it through to the next filter, supported parameters are: \n .P\n .RS 14\n .I\n file\n-=(output, required, io)\n+=(required, output, io)\n .RS 2\n name of the output file to save the image too..\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .TP 10\n@@ -1293,15 +1293,15 @@\n .TP 10\n .B transform\n Transform the input image with the given transformation., supported parameters are: \n .P\n .RS 14\n .I\n file\n-=(input, required, io)\n+=(required, input, io)\n .RS 2\n Name of the file containing the transformation..\n For supported file types see PLUGINS:2dtransform/io\n \n .RE\n .RE\n .TP 10\n"}]}, {"source1": "./usr/share/man/man1/mia-2dimageregistration.1.gz", "source2": "./usr/share/man/man1/mia-2dimageregistration.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dimageregistration.1", "source2": "mia-2dimageregistration.1", "unified_diff": "@@ -15,15 +15,15 @@\n For supported file types see PLUGINS:2dimage/io\n .IP \"\\-r \\-\\-ref-image=(required, input); io\"\n reference image to be registered to\n For supported file types see PLUGINS:2dimage/io\n .IP \"\\-o \\-\\-out-image=(output); io\"\n registered output image\n For supported file types see PLUGINS:2dimage/io\n-.IP \"\\-t \\-\\-transformation=(output, required); io\"\n+.IP \"\\-t \\-\\-transformation=(required, output); io\"\n output transformation comprising the registration\n For supported file types see PLUGINS:2dtransform/io\n .RE\n .SS Help & Info\n .RS\n .IP \"\\-V \\-\\-verbose=warning\"\n verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:\n"}]}, {"source1": "./usr/share/man/man1/mia-2dimageselect.1.gz", "source2": "./usr/share/man/man1/mia-2dimageselect.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dimageselect.1", "source2": "mia-2dimageselect.1", "unified_diff": "@@ -8,15 +8,15 @@\n .B mia\\-2dimageselect\n This program is used to select one 2D images from a multi-image file.\n .SH OPTIONS\n .RS\n .IP \"\\-i \\-\\-in-file=(required, input); io\"\n input images\n For supported file types see PLUGINS:2dimage/io\n-.IP \"\\-o \\-\\-out-file=(output, required); io\"\n+.IP \"\\-o \\-\\-out-file=(required, output); io\"\n output image\n For supported file types see PLUGINS:2dimage/io\n .IP \"\\-n \\-\\-number=0\"\n image number to be selected\n \n .RE\n .SS Help & Info\n"}]}, {"source1": "./usr/share/man/man1/mia-2dimagestats.1.gz", "source2": "./usr/share/man/man1/mia-2dimagestats.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dimagestats.1", "source2": "mia-2dimagestats.1", "unified_diff": "@@ -5,15 +5,15 @@\n .SH SYNOPSIS\n .B mia\\-2dimagestats \\-i [options]\n .SH DESCRIPTION\n .B mia\\-2dimagestats\n 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\n .SH OPTIONS\n .RS\n-.IP \"\\-i \\-\\-in-file=(input, required); io\"\n+.IP \"\\-i \\-\\-in-file=(required, input); io\"\n input image to be analyzed\n For supported file types see PLUGINS:2dimage/io\n .IP \"\\-t \\-\\-thresh=10\"\n intensity thresh to ignore\n \n .IP \"\\-g \\-\\-high-thresh=0.05\"\n upper histogram percentage to ignore\n"}]}, {"source1": "./usr/share/man/man1/mia-2dlerp.1.gz", "source2": "./usr/share/man/man1/mia-2dlerp.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dlerp.1", "source2": "mia-2dlerp.1", "unified_diff": "@@ -5,18 +5,18 @@\n .SH SYNOPSIS\n .B mia\\-2dlerp \\-1 \\-2 \\-o \\-p [options]\n .SH DESCRIPTION\n .B mia\\-2dlerp\n Merge two images by pixel-wise linearly combining their intensities.\n .SH OPTIONS\n .RS\n-.IP \"\\-1 \\-\\-first=(required, input); io\"\n+.IP \"\\-1 \\-\\-first=(input, required); io\"\n first input image \n For supported file types see PLUGINS:2dimage/io\n-.IP \"\\-2 \\-\\-second=(required, input); io\"\n+.IP \"\\-2 \\-\\-second=(input, required); io\"\n second input image \n For supported file types see PLUGINS:2dimage/io\n .IP \"\\-o \\-\\-out-file=(required, output); io\"\n output vector field\n For supported file types see PLUGINS:2dimage/io\n .IP \"\\-p \\-\\-positions=(required); vfloat\"\n image series positions (first, target, second)\n"}]}, {"source1": "./usr/share/man/man1/mia-2dmany2one-nonrigid.1.gz", "source2": "./usr/share/man/man1/mia-2dmany2one-nonrigid.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dmany2one-nonrigid.1", "source2": "mia-2dmany2one-nonrigid.1", "unified_diff": "@@ -7,18 +7,18 @@\n .SH DESCRIPTION\n .B mia\\-2dmany2one\\-nonrigid\n This program registers all images of a conscutively numbered set of images to one common user defined reference.\n .SH OPTIONS\n .SS \n File-IO\n .RS\n-.IP \"\\-i \\-\\-in-file=(input, required); string\"\n+.IP \"\\-i \\-\\-in-file=(required, input); string\"\n input perfusion data set\n \n-.IP \"\\-o \\-\\-out-file=(output, required); string\"\n+.IP \"\\-o \\-\\-out-file=(required, output); string\"\n file name for registered images, numbering and pattern are deducted from the input data\n \n .RE\n .SS \n Registration\n .RS\n .IP \"\\-O \\-\\-optimizer=gsl:opt=gd,step=0.1\"\n"}]}, {"source1": "./usr/share/man/man1/mia-2dmultiimageregistration.1.gz", "source2": "./usr/share/man/man1/mia-2dmultiimageregistration.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dmultiimageregistration.1", "source2": "mia-2dmultiimageregistration.1", "unified_diff": "@@ -5,15 +5,15 @@\n .SH SYNOPSIS\n .B mia\\-2dmultiimageregistration \\-o [options] \n .SH DESCRIPTION\n .B mia\\-2dmultiimageregistration\n 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)\n .SH OPTIONS\n .RS\n-.IP \"\\-o \\-\\-out-transform=(required, output); io\"\n+.IP \"\\-o \\-\\-out-transform=(output, required); io\"\n output transformation\n For supported file types see PLUGINS:2dtransform/io\n .IP \"\\-l \\-\\-levels=3\"\n multi\\-resolution levels\n \n .IP \"\\-O \\-\\-optimizer=gsl:opt=gd,step=0.1\"\n Optimizer used for minimization\n"}]}, {"source1": "./usr/share/man/man1/mia-2dmultiimageto3d.1.gz", "source2": "./usr/share/man/man1/mia-2dmultiimageto3d.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dmultiimageto3d.1", "source2": "mia-2dmultiimageto3d.1", "unified_diff": "@@ -5,18 +5,18 @@\n .SH SYNOPSIS\n .B mia\\-2dmultiimageto3d \\-i \\-o [options]\n .SH DESCRIPTION\n .B mia\\-2dmultiimageto3d\n This program is used to convert a 2D multi-image file to a 3D image.\n .SH OPTIONS\n .RS\n-.IP \"\\-i \\-\\-in-file=(required, input); io\"\n+.IP \"\\-i \\-\\-in-file=(input, required); io\"\n input images\n For supported file types see PLUGINS:2dimage/io\n-.IP \"\\-o \\-\\-out-file=(required, output); io\"\n+.IP \"\\-o \\-\\-out-file=(output, required); io\"\n output image\n For supported file types see PLUGINS:3dimage/io\n .RE\n .SS Help & Info\n .RS\n .IP \"\\-V \\-\\-verbose=warning\"\n verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:\n"}]}, {"source1": "./usr/share/man/man1/mia-2dmultiimagevar.1.gz", "source2": "./usr/share/man/man1/mia-2dmultiimagevar.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dmultiimagevar.1", "source2": "mia-2dmultiimagevar.1", "unified_diff": "@@ -5,15 +5,15 @@\n .SH SYNOPSIS\n .B mia\\-2dmultiimagevar \\-o [options] \n .SH DESCRIPTION\n .B mia\\-2dmultiimagevar\n 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.\n .SH OPTIONS\n .RS\n-.IP \"\\-o \\-\\-out-file=(required, output); io\"\n+.IP \"\\-o \\-\\-out-file=(output, required); io\"\n output image \n For supported file types see PLUGINS:2dimage/io\n .RE\n .SS Help & Info\n .RS\n .IP \"\\-V \\-\\-verbose=warning\"\n verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:\n"}]}, {"source1": "./usr/share/man/man1/mia-2dmyocard-ica.1.gz", "source2": "./usr/share/man/man1/mia-2dmyocard-ica.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dmyocard-ica.1", "source2": "mia-2dmyocard-ica.1", "unified_diff": "@@ -6,15 +6,15 @@\n .B mia\\-2dmyocard\\-ica \\-i [options]\n .SH DESCRIPTION\n .B mia\\-2dmyocard\\-ica\n 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.\n This program is essentially used to test different options on how to run the ICA forreference image creation.\n .SH OPTIONS\n .RS\n-.IP \"\\-i \\-\\-in-base=(required, input); io\"\n+.IP \"\\-i \\-\\-in-base=(input, required); io\"\n input file name ofolloing pattern nameXXXX.ext X=numbers\n For supported file types see PLUGINS:2dimage/io\n .IP \" \\-\\-coefs=\"\n output mixing coefficients to this file\n \n .IP \"\\-o \\-\\-out-base=(output); string\"\n output file name base\n"}]}, {"source1": "./usr/share/man/man1/mia-2dmyocard-icaseries.1.gz", "source2": "./usr/share/man/man1/mia-2dmyocard-icaseries.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dmyocard-icaseries.1", "source2": "mia-2dmyocard-icaseries.1", "unified_diff": "@@ -6,15 +6,15 @@\n .B mia\\-2dmyocard\\-icaseries \\-i [options]\n .SH DESCRIPTION\n .B mia\\-2dmyocard\\-icaseries\n 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.\n .SH OPTIONS\n .SS File-IO\n .RS\n-.IP \"\\-i \\-\\-in-file=(required, input); string\"\n+.IP \"\\-i \\-\\-in-file=(input, required); string\"\n input perfusion data set\n \n .IP \"\\-r \\-\\-references=(output); string\"\n File name base for the reference images. Image type and numbering scheme are taken from the input images.\n \n .IP \"\\-c \\-\\-save-cropped=(output); string\"\n save cropped set of the original set to this file, the image files will use the stem of the name as file name base\n"}]}, {"source1": "./usr/share/man/man1/mia-2dmyocard-segment.1.gz", "source2": "./usr/share/man/man1/mia-2dmyocard-segment.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dmyocard-segment.1", "source2": "mia-2dmyocard-segment.1", "unified_diff": "@@ -9,15 +9,15 @@\n This program is work in progress\n .SH OPTIONS\n .SS File-IO\n .RS\n .IP \"\\-i \\-\\-in-file=(required, input); string\"\n input perfusion data set\n \n-.IP \"\\-o \\-\\-out-file=(output, required); io\"\n+.IP \"\\-o \\-\\-out-file=(required, output); io\"\n output myocardial mask\n For supported file types see PLUGINS:2dimage/io\n .IP \"\\-f \\-\\-save-features=(output); string\"\n save ICA features to files with this name base\n \n .RE\n .SS Help & Info\n"}]}, {"source1": "./usr/share/man/man1/mia-2dmyoica-full.1.gz", "source2": "./usr/share/man/man1/mia-2dmyoica-full.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dmyoica-full.1", "source2": "mia-2dmyoica-full.1", "unified_diff": "@@ -17,15 +17,15 @@\n 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.\n .SH OPTIONS\n .SS File-IO\n .RS\n .IP \"\\-i \\-\\-in-file=(required, input); string\"\n input perfusion data set\n \n-.IP \"\\-o \\-\\-out-file=(output, required); string\"\n+.IP \"\\-o \\-\\-out-file=(required, output); string\"\n output perfusion data set\n \n .IP \"\\-r \\-\\-registered=\"\n 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.\n \n .IP \" \\-\\-save-cropped=(output); string\"\n save cropped set to this file, the image files will use the stem of the name as file name base\n"}]}, {"source1": "./usr/share/man/man1/mia-2dmyoica-nonrigid-parallel.1.gz", "source2": "./usr/share/man/man1/mia-2dmyoica-nonrigid-parallel.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dmyoica-nonrigid-parallel.1", "source2": "mia-2dmyoica-nonrigid-parallel.1", "unified_diff": "@@ -14,15 +14,15 @@\n .UE\n .RE\n \n This version of the program runs all registrations in parallel.\n .SH OPTIONS\n .SS File-IO\n .RS\n-.IP \"\\-i \\-\\-in-file=(required, input); string\"\n+.IP \"\\-i \\-\\-in-file=(input, required); string\"\n input perfusion data set\n \n .IP \"\\-o \\-\\-out-file=(output, required); string\"\n output perfusion data set\n \n .IP \"\\-r \\-\\-registered=reg\"\n 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.\n"}]}, {"source1": "./usr/share/man/man1/mia-2dmyoica-nonrigid.1.gz", "source2": "./usr/share/man/man1/mia-2dmyoica-nonrigid.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dmyoica-nonrigid.1", "source2": "mia-2dmyoica-nonrigid.1", "unified_diff": "@@ -13,15 +13,15 @@\n Wollny G, Kellman P, Santos A, Ledesma-Carbayo M-J, \"Automatic Motion Compensation of Free Breathing acquired Myocardial Perfusion Data by using Independent Component Analysis\" Medical Image Analysis, 2012.\n .UE\n .RE\n \n .SH OPTIONS\n .SS File-IO\n .RS\n-.IP \"\\-i \\-\\-in-file=(required, input); string\"\n+.IP \"\\-i \\-\\-in-file=(input, required); string\"\n input perfusion data set\n \n .IP \"\\-o \\-\\-out-file=(required, output); string\"\n output perfusion data set\n \n .IP \"\\-r \\-\\-registered=reg\"\n file name base for registered fiels\n"}]}, {"source1": "./usr/share/man/man1/mia-2dmyoica-nonrigid2.1.gz", "source2": "./usr/share/man/man1/mia-2dmyoica-nonrigid2.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dmyoica-nonrigid2.1", "source2": "mia-2dmyoica-nonrigid2.1", "unified_diff": "@@ -8,18 +8,18 @@\n .B mia\\-2dmyoica\\-nonrigid2\n This program runs the non-rigid registration of an perfusion image series.In each pass, first an ICA analysis is run to estimate and eliminate the periodic movement and create reference images with intensities similar to the corresponding original image. Then non-rigid registration is run using the an \"ssd + divcurl\" cost model. The B-spline c-rate and the divcurl cost weight are changed in each pass according to given parameters.In the first pass a bounding box around the LV myocardium may be extractedto speed up computation\n Special note to this implemnentation: the registration is always run from the original images to avoid the accumulation of interpolation errors.\n .SH OPTIONS\n .SS \n File-IO\n .RS\n-.IP \"\\-i \\-\\-in-file=(required, input); string\"\n+.IP \"\\-i \\-\\-in-file=(input, required); string\"\n input perfusion data set\n \n-.IP \"\\-o \\-\\-out-file=(required, output); string\"\n+.IP \"\\-o \\-\\-out-file=(output, required); string\"\n output perfusion data set\n \n .IP \"\\-r \\-\\-registered=reg\"\n file name base for registered fiels\n \n .IP \" \\-\\-save-cropped=\"\n save cropped set to this file\n"}]}, {"source1": "./usr/share/man/man1/mia-2dmyomilles.1.gz", "source2": "./usr/share/man/man1/mia-2dmyomilles.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dmyomilles.1", "source2": "mia-2dmyomilles.1", "unified_diff": "@@ -15,15 +15,15 @@\n .RE\n \n Changes include the extraction of the quasi-periodic movement in free breathingly acquired data sets and the option to run affine or rigid registration instead of the optimization of translations only.\n \n .SH OPTIONS\n .SS File-IO\n .RS\n-.IP \"\\-i \\-\\-in-file=(required, input); string\"\n+.IP \"\\-i \\-\\-in-file=(input, required); string\"\n input perfusion data set\n \n .IP \"\\-o \\-\\-out-file=(required, output); string\"\n output perfusion data set\n \n .IP \"\\-r \\-\\-registered=\"\n file name base for registered files\n"}]}, {"source1": "./usr/share/man/man1/mia-2dmyoperiodic-nonrigid.1.gz", "source2": "./usr/share/man/man1/mia-2dmyoperiodic-nonrigid.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dmyoperiodic-nonrigid.1", "source2": "mia-2dmyoperiodic-nonrigid.1", "unified_diff": "@@ -17,15 +17,15 @@\n .SH OPTIONS\n .SS \n File-IO\n .RS\n .IP \"\\-i \\-\\-in-file=(required, input); string\"\n input perfusion data set\n \n-.IP \"\\-o \\-\\-out-file=(output, required); string\"\n+.IP \"\\-o \\-\\-out-file=(required, output); string\"\n output perfusion data set\n \n .IP \"\\-r \\-\\-registered=reg\"\n file name base for registered fiels\n \n .IP \" \\-\\-save-references\"\n Save synthetic references to files refXXXX.v\n"}]}, {"source1": "./usr/share/man/man1/mia-2dmyopgt-nonrigid.1.gz", "source2": "./usr/share/man/man1/mia-2dmyopgt-nonrigid.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dmyopgt-nonrigid.1", "source2": "mia-2dmyopgt-nonrigid.1", "unified_diff": "@@ -15,15 +15,15 @@\n .RE\n \n . Note that for this nonlinear motion correction a preceding linear registration step is usually required.\n .SH OPTIONS\n .SS \n File-IO\n .RS\n-.IP \"\\-i \\-\\-in-file=(required, input); string\"\n+.IP \"\\-i \\-\\-in-file=(input, required); string\"\n input perfusion data set\n \n .IP \"\\-o \\-\\-out-file=(output, required); string\"\n output perfusion data set\n \n .IP \"\\-r \\-\\-registered=reg\"\n file name base for registered files, the image file type is the same as given in the input data set\n"}]}, {"source1": "./usr/share/man/man1/mia-2dmyoserial-nonrigid.1.gz", "source2": "./usr/share/man/man1/mia-2dmyoserial-nonrigid.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dmyoserial-nonrigid.1", "source2": "mia-2dmyoserial-nonrigid.1", "unified_diff": "@@ -17,15 +17,15 @@\n .SH OPTIONS\n .SS \n File-IO\n .RS\n .IP \"\\-i \\-\\-in-file=(required, input); string\"\n input perfusion data set\n \n-.IP \"\\-o \\-\\-out-file=(required, output); string\"\n+.IP \"\\-o \\-\\-out-file=(output, required); string\"\n output perfusion data set\n \n .IP \"\\-R \\-\\-registered=reg\"\n file name base for registered fiels\n \n .RE\n .SS \n"}]}, {"source1": "./usr/share/man/man1/mia-2dmyoseries-compdice.1.gz", "source2": "./usr/share/man/man1/mia-2dmyoseries-compdice.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dmyoseries-compdice.1", "source2": "mia-2dmyoseries-compdice.1", "unified_diff": "@@ -5,18 +5,18 @@\n .SH SYNOPSIS\n .B mia\\-2dmyoseries\\-compdice \\-1 \\-2 [options]\n .SH DESCRIPTION\n .B mia\\-2dmyoseries\\-compdice\n This program is used to evaluate the per-frame dice index of segmented regions of two image series\n .SH OPTIONS\n .RS\n-.IP \"\\-1 \\-\\-first=(input, required); string\"\n+.IP \"\\-1 \\-\\-first=(required, input); string\"\n first segmentation set\n \n-.IP \"\\-2 \\-\\-second=(input, required); string\"\n+.IP \"\\-2 \\-\\-second=(required, input); string\"\n second segmentation set\n \n .IP \"\\-k \\-\\-skip=2\"\n images to skip atthe begin of the series\n \n .RE\n .SS Help & Info\n"}]}, {"source1": "./usr/share/man/man1/mia-2dmyoset-all2one-nonrigid.1.gz", "source2": "./usr/share/man/man1/mia-2dmyoset-all2one-nonrigid.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dmyoset-all2one-nonrigid.1", "source2": "mia-2dmyoset-all2one-nonrigid.1", "unified_diff": "@@ -10,15 +10,15 @@\n .SH OPTIONS\n .SS \n File-IO\n .RS\n .IP \"\\-i \\-\\-in-file=(required, input); string\"\n input perfusion data set\n \n-.IP \"\\-o \\-\\-out-file=(output, required); string\"\n+.IP \"\\-o \\-\\-out-file=(required, output); string\"\n output perfusion data set\n \n .IP \" \\-\\-out-filebase=reg\"\n file name basae for registered files, file type is deducted from the image file type in the input data set.\n \n .RE\n .SS \n"}]}, {"source1": "./usr/share/man/man1/mia-2dseghausdorff.1.gz", "source2": "./usr/share/man/man1/mia-2dseghausdorff.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dseghausdorff.1", "source2": "mia-2dseghausdorff.1", "unified_diff": "@@ -5,15 +5,15 @@\n .SH SYNOPSIS\n .B mia\\-2dseghausdorff \\-i \\-r [options]\n .SH DESCRIPTION\n .B mia\\-2dseghausdorff\n Get the per-slice Hausdorff distance of a segmentation with respect to a given reference frame and print it to stdout.\n .SH OPTIONS\n .RS\n-.IP \"\\-i \\-\\-in-file=(input, required); string\"\n+.IP \"\\-i \\-\\-in-file=(required, input); string\"\n input segmentation set\n \n .IP \"\\-r \\-\\-ref-frame=(required); ulong\"\n reference frame\n \n .IP \"\\-k \\-\\-skip=0\"\n skip frames at the beginning\n"}]}, {"source1": "./usr/share/man/man1/mia-2dsegment-ahmed.1.gz", "source2": "./usr/share/man/man1/mia-2dsegment-ahmed.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dsegment-ahmed.1", "source2": "mia-2dsegment-ahmed.1", "unified_diff": "@@ -13,18 +13,18 @@\n 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,\n .UE\n .RE\n \n changes are: p=2, and exp\n .SH OPTIONS\n .RS\n-.IP \"\\-i \\-\\-in-file=(required, input); io\"\n+.IP \"\\-i \\-\\-in-file=(input, required); io\"\n image to be segmented\n For supported file types see PLUGINS:2dimage/io\n-.IP \"\\-o \\-\\-out-file=(required, output); io\"\n+.IP \"\\-o \\-\\-out-file=(output, required); io\"\n class probability images, the image type must support multiple images and floating point values\n For supported file types see PLUGINS:2dimage/io\n .IP \"\\-a \\-\\-no-of-classes=3\"\n number of classes\n \n .IP \"\\-b \\-\\-bias-correct\"\n apply bias field correction\n"}]}, {"source1": "./usr/share/man/man1/mia-2dsegment-local-cmeans.1.gz", "source2": "./usr/share/man/man1/mia-2dsegment-local-cmeans.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dsegment-local-cmeans.1", "source2": "mia-2dsegment-local-cmeans.1", "unified_diff": "@@ -13,15 +13,15 @@\n Dunmore CJ, Wollny G, Skinner MM. (2018) MIA-Clustering: a novel method for segmentation of paleontological material. PeerJ 6:e4374.\n .UE\n .RE\n \n .SH OPTIONS\n .SS File-IO\n .RS\n-.IP \"\\-i \\-\\-in-file=(required, input); io\"\n+.IP \"\\-i \\-\\-in-file=(input, required); io\"\n image to be segmented\n For supported file types see PLUGINS:2dimage/io\n .IP \"\\-o \\-\\-out-file=(output); io\"\n class label image based on merging local labels\n For supported file types see PLUGINS:2dimage/io\n .IP \"\\-G \\-\\-out-global-crisp=(output); io\"\n class label image based on global segmentation\n"}]}, {"source1": "./usr/share/man/man1/mia-2dsegment-per-pixel-kmeans.1.gz", "source2": "./usr/share/man/man1/mia-2dsegment-per-pixel-kmeans.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dsegment-per-pixel-kmeans.1", "source2": "mia-2dsegment-per-pixel-kmeans.1", "unified_diff": "@@ -9,15 +9,15 @@\n This program runs the segmentation of a 2D image by applying a localized k-means approach that helps to overcome intensity inhomogeneities in the image. The approach evaluates a global k-means clustering, and then separates the image into overlapping regions where more k-means iterations are run only including the locally present classes, i.e. the classes that relatively contain more pixels than a given threshold.\n .SH OPTIONS\n .SS File-IO\n .RS\n .IP \"\\-i \\-\\-in-file=(required, input); io\"\n image to be segmented\n For supported file types see PLUGINS:2dimage/io\n-.IP \"\\-o \\-\\-out-file=(required, output); io\"\n+.IP \"\\-o \\-\\-out-file=(output, required); io\"\n class label image based on merging local labels\n For supported file types see PLUGINS:2dimage/io\n .RE\n .SS Help & Info\n .RS\n .IP \"\\-V \\-\\-verbose=warning\"\n verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:\n"}]}, {"source1": "./usr/share/man/man1/mia-2dsegshift.1.gz", "source2": "./usr/share/man/man1/mia-2dsegshift.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dsegshift.1", "source2": "mia-2dsegshift.1", "unified_diff": "@@ -5,18 +5,18 @@\n .SH SYNOPSIS\n .B mia\\-2dsegshift \\-i \\-o [options]\n .SH DESCRIPTION\n .B mia\\-2dsegshift\n 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.\n .SH OPTIONS\n .RS\n-.IP \"\\-i \\-\\-in-file=(required, input); io\"\n+.IP \"\\-i \\-\\-in-file=(input, required); io\"\n input segmentation set\n For supported file types see PLUGINS:2dimage/io\n-.IP \"\\-o \\-\\-out-file=(output, required); io\"\n+.IP \"\\-o \\-\\-out-file=(required, output); io\"\n input segmentation set\n For supported file types see PLUGINS:2dimage/io\n .IP \"\\-g \\-\\-image-file=crop\"\n output image filename base\n \n .IP \"\\-S \\-\\-shift=[0,0]\"\n shift of segmentation\n"}]}, {"source1": "./usr/share/man/man1/mia-2dsegshiftperslice.1.gz", "source2": "./usr/share/man/man1/mia-2dsegshiftperslice.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dsegshiftperslice.1", "source2": "mia-2dsegshiftperslice.1", "unified_diff": "@@ -8,15 +8,15 @@\n .B mia\\-2dsegshiftperslice\n 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. \n .SH OPTIONS\n .RS\n .IP \"\\-i \\-\\-in-file=(required, input); string\"\n input segmentation set\n \n-.IP \"\\-o \\-\\-out-file=(required, output); string\"\n+.IP \"\\-o \\-\\-out-file=(output, required); string\"\n output segmentation set\n \n .IP \"\\-g \\-\\-image-file=crop\"\n output image filename base\n \n .IP \"\\-S \\-\\-shift=(required); string\"\n shift of segmentation \\- base name \n"}]}, {"source1": "./usr/share/man/man1/mia-2dseries-mincorr.1.gz", "source2": "./usr/share/man/man1/mia-2dseries-mincorr.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dseries-mincorr.1", "source2": "mia-2dseries-mincorr.1", "unified_diff": "@@ -8,15 +8,15 @@\n .B mia\\-2dseries\\-mincorr\n Given a set of images of temporal sucession, this program evaluates the minimal correlation of the time-intensity curve between neighboring pixels.\n .SH OPTIONS\n .RS\n .IP \"\\-i \\-\\-in-set=(required, input); string\"\n input segmentation set\n \n-.IP \"\\-o \\-\\-out-set=(required, output); io\"\n+.IP \"\\-o \\-\\-out-set=(output, required); io\"\n output image of minimal correlation\n For supported file types see PLUGINS:2dimage/io\n .IP \"\\-k \\-\\-skip=2\"\n skip images at beginning of series\n \n .RE\n .SS Help & Info\n"}]}, {"source1": "./usr/share/man/man1/mia-2dseries-segdistance.1.gz", "source2": "./usr/share/man/man1/mia-2dseries-segdistance.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dseries-segdistance.1", "source2": "mia-2dseries-segdistance.1", "unified_diff": "@@ -5,15 +5,15 @@\n .SH SYNOPSIS\n .B mia\\-2dseries\\-segdistance \\-i [options]\n .SH DESCRIPTION\n .B mia\\-2dseries\\-segdistance\n Get the mean distance of a segmentation boundary to the reference boundary.\n .SH OPTIONS\n .RS\n-.IP \"\\-i \\-\\-in-file=(required, input); string\"\n+.IP \"\\-i \\-\\-in-file=(input, required); string\"\n input segmentation set\n \n .IP \"\\-r \\-\\-reference=20\"\n reference frame\n \n .IP \"\\-k \\-\\-skip=0\"\n skip images at the beginning\n"}]}, {"source1": "./usr/share/man/man1/mia-2dseries2sets.1.gz", "source2": "./usr/share/man/man1/mia-2dseries2sets.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dseries2sets.1", "source2": "mia-2dseries2sets.1", "unified_diff": "@@ -5,15 +5,15 @@\n .SH SYNOPSIS\n .B mia\\-2dseries2sets \\-o [options] \n .SH DESCRIPTION\n .B mia\\-2dseries2sets\n 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 taylored to used 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.\n .SH OPTIONS\n .RS\n-.IP \"\\-o \\-\\-out-directory=(required, output); string\"\n+.IP \"\\-o \\-\\-out-directory=(output, required); string\"\n output directory (needs to exist and be writable)\n \n .IP \" \\-\\-no-copy\"\n don't copy image files to output directory\n \n .RE\n .SS Help & Info\n"}]}, {"source1": "./usr/share/man/man1/mia-2dseriesgradMAD.1.gz", "source2": "./usr/share/man/man1/mia-2dseriesgradMAD.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dseriesgradMAD.1", "source2": "mia-2dseriesgradMAD.1", "unified_diff": "@@ -5,18 +5,18 @@\n .SH SYNOPSIS\n .B mia\\-2dseriesgradMAD \\-i \\-o [options] \n .SH DESCRIPTION\n .B mia\\-2dseriesgradMAD\n Given a set of images of temporal sucession, evaluates the pixel-wise temporal gradient and then its median average distance (MAD) and stores the result in an image. Spacial pre-filtering may be applied as given additional plugin(s) (filter/2dimage).\n .SH OPTIONS\n .RS\n-.IP \"\\-i \\-\\-in-file=(required, input); string\"\n+.IP \"\\-i \\-\\-in-file=(input, required); string\"\n input segmentation set\n \n-.IP \"\\-o \\-\\-out-file=(required, output); io\"\n+.IP \"\\-o \\-\\-out-file=(output, required); io\"\n output file name\n For supported file types see PLUGINS:2dimage/io\n .IP \"\\-k \\-\\-skip=0\"\n Skip files at the beginning\n \n .IP \"\\-e \\-\\-enlarge-boundary=5\"\n Enlarge cropbox by number of pixels\n@@ -355,15 +355,15 @@\n .TP 10\n .B combiner\n 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: \n .P\n .RS 14\n .I\n image\n-=(required, input, io)\n+=(input, required, io)\n .RS 2\n second image that is needed in the combiner.\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .RS 14\n@@ -699,15 +699,15 @@\n .TP 10\n .B labelmap\n Image filter to remap label id's. Only applicable to images with integer valued intensities/labels., supported parameters are: \n .P\n .RS 14\n .I\n map\n-=(required, input, string)\n+=(input, required, string)\n .RS 2\n Label mapping file.\n \n .RE\n .RE\n .TP 10\n .B labelscale\n@@ -725,15 +725,15 @@\n .TP 10\n .B load\n Load the input image from a file and use it to replace the current image in the pipeline., supported parameters are: \n .P\n .RS 14\n .I\n file\n-=(required, input, io)\n+=(input, required, io)\n .RS 2\n name of the input file to load from..\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .TP 10\n@@ -764,15 +764,15 @@\n .RE\n \n .RE\n .RE\n .RS 14\n .I\n input\n-=(required, input, io)\n+=(input, required, io)\n .RS 2\n second input image file name.\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .RS 14\n@@ -787,25 +787,25 @@\n .TP 10\n .B maxflow\n This filter implements the uses the max-flow min-cut algorithmfor image segmentation, supported parameters are: \n .P\n .RS 14\n .I\n sink-flow\n-=(required, input, io)\n+=(input, required, io)\n .RS 2\n Image of float type to define the per\\-pixel flow to the sink.\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .RS 14\n .I\n source-flow\n-=(required, input, io)\n+=(input, required, io)\n .RS 2\n Image of float type to define the per\\-pixel flow to the source.\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .TP 10\n@@ -833,15 +833,15 @@\n Intensity thresholding parameter: Pixels with intensities below this threshold will be set to zero, and also not used when evaluating mean and variation.\n \n .RE\n .RE\n .RS 14\n .I\n varfile\n-=(required, output, io)\n+=(output, required, io)\n .RS 2\n name of the output file to save the variation image too..\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .RS 14\n@@ -869,15 +869,15 @@\n .TP 10\n .B medianmad\n 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: \n .P\n .RS 14\n .I\n madfile\n-=(required, output, io)\n+=(output, required, io)\n .RS 2\n name of the output file to save the median absolute deviation image too..\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .RS 14\n@@ -994,15 +994,15 @@\n For supported plug-ins see PLUGINS:2dimage/shape\n \n .RE\n .RE\n .RS 14\n .I\n seed\n-=(required, input, io)\n+=(input, required, io)\n .RS 2\n seed image (bit valued).\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .TP 10\n@@ -1175,28 +1175,28 @@\n For supported plug-ins see PLUGINS:2dimage/shape\n \n .RE\n .RE\n .RS 14\n .I\n seed\n-=(required, input, string)\n+=(input, required, string)\n .RS 2\n seed input image containing the lables for the initial regions.\n \n .RE\n .RE\n .TP 10\n .B tee\n Save the input image to a file and also pass it through to the next filter, supported parameters are: \n .P\n .RS 14\n .I\n file\n-=(required, output, io)\n+=(output, required, io)\n .RS 2\n name of the output file to save the image too..\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .TP 10\n@@ -1260,15 +1260,15 @@\n .TP 10\n .B transform\n Transform the input image with the given transformation., supported parameters are: \n .P\n .RS 14\n .I\n file\n-=(required, input, io)\n+=(input, required, io)\n .RS 2\n Name of the file containing the transformation..\n For supported file types see PLUGINS:2dtransform/io\n \n .RE\n .RE\n .TP 10\n"}]}, {"source1": "./usr/share/man/man1/mia-2dseriesgradvariation.1.gz", "source2": "./usr/share/man/man1/mia-2dseriesgradvariation.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dseriesgradvariation.1", "source2": "mia-2dseriesgradvariation.1", "unified_diff": "@@ -5,18 +5,18 @@\n .SH SYNOPSIS\n .B mia\\-2dseriesgradvariation \\-i \\-o [options]\n .SH DESCRIPTION\n .B mia\\-2dseriesgradvariation\n Given a set of images of temporal sucession, this program evaluates the gradient variation of the pixel-wise time-intensity curves of this series. If the input image set provides a segmentation, then this segmentation can be used to create a bounding box and restrict evaluation to this box. \n .SH OPTIONS\n .RS\n-.IP \"\\-i \\-\\-in-file=(required, input); string\"\n+.IP \"\\-i \\-\\-in-file=(input, required); string\"\n input segmentation set\n \n-.IP \"\\-o \\-\\-out-file=(required, output); io\"\n+.IP \"\\-o \\-\\-out-file=(output, required); io\"\n output file name\n For supported file types see PLUGINS:2dimage/io\n .IP \"\\-k \\-\\-skip=0\"\n Skip files at the beginning\n \n .IP \"\\-e \\-\\-enlarge-boundary=5\"\n Enlarge cropbox by number of pixels\n"}]}, {"source1": "./usr/share/man/man1/mia-2dserieshausdorff.1.gz", "source2": "./usr/share/man/man1/mia-2dserieshausdorff.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dserieshausdorff.1", "source2": "mia-2dserieshausdorff.1", "unified_diff": "@@ -5,18 +5,18 @@\n .SH SYNOPSIS\n .B mia\\-2dserieshausdorff \\-i \\-r [options]\n .SH DESCRIPTION\n .B mia\\-2dserieshausdorff\n Get the per-slice Hausdorff distance of a segmentation with respect to a given reference segmentation set.\n .SH OPTIONS\n .RS\n-.IP \"\\-i \\-\\-in-file=(input, required); string\"\n+.IP \"\\-i \\-\\-in-file=(required, input); string\"\n input segmentation set\n \n-.IP \"\\-r \\-\\-ref-file=(input, required); string\"\n+.IP \"\\-r \\-\\-ref-file=(required, input); string\"\n reference segmentation set\n \n .IP \"\\-k \\-\\-skip=0\"\n skip images at the beginning\n \n .RE\n .SS Help & Info\n"}]}, {"source1": "./usr/share/man/man1/mia-2dseriessmoothgradMAD.1.gz", "source2": "./usr/share/man/man1/mia-2dseriessmoothgradMAD.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dseriessmoothgradMAD.1", "source2": "mia-2dseriessmoothgradMAD.1", "unified_diff": "@@ -5,15 +5,15 @@\n .SH SYNOPSIS\n .B mia\\-2dseriessmoothgradMAD \\-i \\-o [options] \n .SH DESCRIPTION\n .B mia\\-2dseriessmoothgradMAD\n Given a set of images of temporal sucession, 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)\n .SH OPTIONS\n .RS\n-.IP \"\\-i \\-\\-in-file=(input, required); string\"\n+.IP \"\\-i \\-\\-in-file=(required, input); string\"\n input segmentation set\n \n .IP \"\\-o \\-\\-out-file=(required, output); io\"\n output file name\n For supported file types see PLUGINS:2dimage/io\n .IP \"\\-k \\-\\-skip=0\"\n Skip files at the beginning\n@@ -358,15 +358,15 @@\n .TP 10\n .B combiner\n 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: \n .P\n .RS 14\n .I\n image\n-=(input, required, io)\n+=(required, input, io)\n .RS 2\n second image that is needed in the combiner.\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .RS 14\n@@ -702,15 +702,15 @@\n .TP 10\n .B labelmap\n Image filter to remap label id's. Only applicable to images with integer valued intensities/labels., supported parameters are: \n .P\n .RS 14\n .I\n map\n-=(input, required, string)\n+=(required, input, string)\n .RS 2\n Label mapping file.\n \n .RE\n .RE\n .TP 10\n .B labelscale\n@@ -728,15 +728,15 @@\n .TP 10\n .B load\n Load the input image from a file and use it to replace the current image in the pipeline., supported parameters are: \n .P\n .RS 14\n .I\n file\n-=(input, required, io)\n+=(required, input, io)\n .RS 2\n name of the input file to load from..\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .TP 10\n@@ -767,15 +767,15 @@\n .RE\n \n .RE\n .RE\n .RS 14\n .I\n input\n-=(input, required, io)\n+=(required, input, io)\n .RS 2\n second input image file name.\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .RS 14\n@@ -790,25 +790,25 @@\n .TP 10\n .B maxflow\n This filter implements the uses the max-flow min-cut algorithmfor image segmentation, supported parameters are: \n .P\n .RS 14\n .I\n sink-flow\n-=(input, required, io)\n+=(required, input, io)\n .RS 2\n Image of float type to define the per\\-pixel flow to the sink.\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .RS 14\n .I\n source-flow\n-=(input, required, io)\n+=(required, input, io)\n .RS 2\n Image of float type to define the per\\-pixel flow to the source.\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .TP 10\n@@ -997,15 +997,15 @@\n For supported plug-ins see PLUGINS:2dimage/shape\n \n .RE\n .RE\n .RS 14\n .I\n seed\n-=(input, required, io)\n+=(required, input, io)\n .RS 2\n seed image (bit valued).\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .TP 10\n@@ -1178,15 +1178,15 @@\n For supported plug-ins see PLUGINS:2dimage/shape\n \n .RE\n .RE\n .RS 14\n .I\n seed\n-=(input, required, string)\n+=(required, input, string)\n .RS 2\n seed input image containing the lables for the initial regions.\n \n .RE\n .RE\n .TP 10\n .B tee\n@@ -1263,15 +1263,15 @@\n .TP 10\n .B transform\n Transform the input image with the given transformation., supported parameters are: \n .P\n .RS 14\n .I\n file\n-=(input, required, io)\n+=(required, input, io)\n .RS 2\n Name of the file containing the transformation..\n For supported file types see PLUGINS:2dtransform/io\n \n .RE\n .RE\n .TP 10\n"}]}, {"source1": "./usr/share/man/man1/mia-2dseriestovolume.1.gz", "source2": "./usr/share/man/man1/mia-2dseriestovolume.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dseriestovolume.1", "source2": "mia-2dseriestovolume.1", "unified_diff": "@@ -8,15 +8,15 @@\n .B mia\\-2dseriestovolume\n Obtaines a 3D volume image by combining the images of the segmentation set.\n .SH OPTIONS\n .RS\n .IP \"\\-i \\-\\-in-file=(required, input); string\"\n input segmentation set\n \n-.IP \"\\-o \\-\\-out-file=(output, required); io\"\n+.IP \"\\-o \\-\\-out-file=(required, output); io\"\n output 3D image \n For supported file types see PLUGINS:3dimage/io\n .IP \"\\-k \\-\\-skip=0\"\n number of frames to skip at the beginning of the series.\n \n .RE\n .SS Help & Info\n"}]}, {"source1": "./usr/share/man/man1/mia-2dstack-cmeans-presegment.1.gz", "source2": "./usr/share/man/man1/mia-2dstack-cmeans-presegment.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dstack-cmeans-presegment.1", "source2": "mia-2dstack-cmeans-presegment.1", "unified_diff": "@@ -6,15 +6,15 @@\n .B mia\\-2dstack\\-cmeans\\-presegment \\-i \\-o \\-L