--- name: "mia-3dforce" 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-3dforce" --- # mia-3dforce(1) Evaluate the registration force between two 3D images. ## NAME mia-3dforce - Evaluate the registration force between two 3D images. ## SYNOPSIS **mia-3dforce -i \ -r \ -o \ \[options\]** ## DESCRIPTION **mia-3dforce** This program is used to create an image comprising the pixel-wise norm of the ggradient of a given cost function. ## OPTIONS - \-i --src-file=(required, input); io input image\ For supported file types see PLUGINS:3dimage/io - \-r --ref-file=(required, input); io output force norm image\ For supported file types see PLUGINS:3dimage/io - \-o --out-file=(output, required); io reference image\ For supported file types see PLUGINS:3dimage/io - \-c --cost=ssd cost function to use\ For supported plugins see PLUGINS:3dimage/cost ### 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: 1d/splinekernel - **bspline** B-spline kernel creation , supported parameters are: *d* = 3; int in \[0, 5\] Spline degree. - **omoms** OMoms-spline kernel creation, supported parameters are: *d* = 3; int in \[3, 3\] Spline degree. ## PLUGINS: 3dimage/cost - **lncc** local normalized cross correlation with masking support., supported parameters are: *w* = 5; uint in \[1, 256\] half width of the window used for evaluating the localized cross correlation. - **mi** Spline parzen based mutual information., supported parameters are: *cut* = 0; float in \[0, 40\] Percentage of pixels to cut at high and low intensities to remove outliers. *mbins* = 64; uint in \[1, 256\] Number of histogram bins used for the moving image. *mkernel* = \[bspline:d=3\]; factory Spline kernel for moving image parzen hinstogram. For supported plug-ins see PLUGINS:1d/splinekernel *rbins* = 64; uint in \[1, 256\] Number of histogram bins used for the reference image. *rkernel* = \[bspline:d=0\]; factory Spline kernel for reference image parzen hinstogram. For supported plug-ins see PLUGINS:1d/splinekernel - **ncc** normalized cross correlation. (no parameters) - **ngf** This function evaluates the image similarity based on normalized gradient fields. Given normalized gradient fields $ \_S$ of the src image and $ \_R$ of the ref image various evaluators are implemented., supported parameters are: *eval* = ds; dict plugin subtype (sq, ds,dot,cross). Supported values are: *ds* ‐ square of scaled difference *dot* ‐ scalar product kernel *cross* ‐ cross product kernel - **ssd** 3D image cost: sum of squared differences, supported parameters are: *autothresh* = 0; float in \[0, 1000\] Use automatic masking of the moving image by only takeing intensity values into accound that are larger than the given threshold. *norm* = 0; bool Set whether the metric should be normalized by the number of image pixels. - **ssd-automask** 3D image cost: sum of squared differences, with automasking based on given thresholds, supported parameters are: *rthresh* = 0; double Threshold intensity value for reference image. *sthresh* = 0; double Threshold intensity value for source image. ## 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 weigtes sum of SSD between src.v and ref.v and store the result in forcenorm.v. mia-3dforce -i src.v -r ref.v -c ssd -o forcenorm.v ## 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'.