--- name: "mia-3ddistance-stats" section: "1" platform: "linux" package: "mia-tools" version: "2.4.7-11+b1" release: "Debian 12 (Bookworm)" platforms: ["linux"] url: "https://new.carta.tech/mia-3ddistance-stats" --- # mia-3ddistance-stats(1) Evaluate distance statistics for two labeled images. ## NAME mia-3ddistance-stats - Evaluate distance statistics for two labeled images. ## SYNOPSIS **mia-3ddistance-stats -i \ -r \ -o \ \[options\]** ## DESCRIPTION **mia-3ddistance-stats** This program is used to evaluate the distance between equally labelled areas in two images. The output file is a csv file containing the distances for each labeled coordinate in the test image in the following form: label,n-samples,distance,distance,... A simple R program to get some per label statistics from this data would look like args \<- commandArgs(TRUE)\ data \<- read.csv(args\[1\], header=FALSE)\ for ( i in 1:dim(data)\[1\] ) {\ line \<- data\[i,\]\ label \<- as.integer(line\[1\])\ end\_range \<- 2 + as.numeric(line\[2\])\ s \<- as.numeric(line\[3:end\_range\])\ result \<- sprintf("%d %8.4f %8.4f %8.4f %8.4f0\ label, mean(s), sqrt(var(s)), median(s), max(s))\ cat(result)\ } ## OPTIONS ### File-IO - \-i --in-labels=(required, input); io input label image\ For supported file types see PLUGINS:3dimage/io - \-r --ref-labels=(required, input); io reference label image\ For supported file types see PLUGINS:3dimage/io - \-l --label-map=(input); string optional mapping of label numbers - \-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. ### Help & Info - \-V --verbose=warning verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are: *trace* ‐ Function call trace *debug* ‐ Debug output *info* ‐ Low level messages *message* ‐ Normal messages *warning* ‐ Warnings *fail* ‐ Report test failures *error* ‐ Report errors *fatal* ‐ Report only fatal errors - \--copyright print copyright information - \-h --help print this help - \-? --usage print a short help - \--version print the version number and exit ### Processing - \--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). ## PLUGINS: 3dimage/io - **analyze** Analyze 7.5 image Recognized file extensions: .HDR, .hdr Supported element types: unsigned 8 bit, signed 16 bit, signed 32 bit, floating point 32 bit, floating point 64 bit - **datapool** Virtual IO to and from the internal data pool Recognized file extensions: .@ - **dicom** Dicom image series as 3D Recognized file extensions: .DCM, .dcm Supported element types: signed 16 bit, unsigned 16 bit - **hdf5** HDF5 3D image IO Recognized file extensions: .H5, .h5 Supported element types: binary data, signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32 bit, unsigned 32 bit, signed 64 bit, unsigned 64 bit, floating point 32 bit, floating point 64 bit - **inria** INRIA image Recognized file extensions: .INR, .inr Supported element types: signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32 bit, unsigned 32 bit, floating point 32 bit, floating point 64 bit - **mhd** MetaIO 3D image IO using the VTK implementation (experimental). Recognized file extensions: .MHA, .MHD, .mha, .mhd Supported element types: signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32 bit, unsigned 32 bit, floating point 32 bit, floating point 64 bit - **nifti** NIFTI-1 3D image IO. The orientation is transformed in the same way like it is done with 'dicomtonifti --no-reorder' from the vtk-dicom package. Recognized file extensions: .NII, .nii Supported element types: signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32 bit, unsigned 32 bit, signed 64 bit, unsigned 64 bit, floating point 32 bit, floating point 64 bit - **vff** VFF Sun raster format Recognized file extensions: .VFF, .vff Supported element types: unsigned 8 bit, signed 16 bit - **vista** Vista 3D Recognized file extensions: .-, .V, .VISTA, .v, .vista Supported element types: binary data, signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32 bit, unsigned 32 bit, floating point 32 bit, floating point 64 bit - **vti** 3D image VTK-XML in- and output (experimental). Recognized file extensions: .VTI, .vti Supported element types: signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32 bit, unsigned 32 bit, floating point 32 bit, floating point 64 bit - **vtk** 3D VTK image legacy in- and output (experimental). Recognized file extensions: .VTK, .VTKIMAGE, .vtk, .vtkimage Supported element types: signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32 bit, unsigned 32 bit, floating point 32 bit, floating point 64 bit ## EXAMPLE Evaluate the distances for each label available in image.v to the corresponding labels in the image reference.v ans store the result a coma separated list of values, i.e. distances.csv. mia-3ddistance-stats -i image.v -r reference.v -o distances.csv ## AUTHOR(s) Gert Wollny ## COPYRIGHT This software is Copyright (c) 1999‐2015 Leipzig, Germany and Madrid, Spain. It comes with ABSOLUTELY NO WARRANTY and you may redistribute it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 (or later). For more information run the program with the option '--copyright'.