--- name: "mia-3ddeform" 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-3ddeform" --- # mia-3ddeform(1) Transform a 3D image by means of a vector field. ## NAME mia-3ddeform - Transform a 3D image by means of a vector field. ## SYNOPSIS **mia-3ddeform -i \ -o \ -t \ \[options\]** ## DESCRIPTION **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) ## OPTIONS - \-i --in-image=(input, required); io input image\ For supported file types see PLUGINS:3dimage/io - \-o --out-image=(required, output); io transformed image\ For supported file types see PLUGINS:3dimage/io - \-t --transformation=(input, required); io transformation vector field\ For supported file types see PLUGINS:3dvf/io - \-p --interpolator=bspline:d=3 image interpolator kernel\ For supported plugins see PLUGINS:1d/splinekernel ### 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/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 ## PLUGINS: 3dvf/io - **cvista** obsolete 3d vector field io plugin for range compressend vista (saving not supported) Recognized file extensions: .CVF, .cvf Supported element types: floating point 32 bit - **datapool** Virtual IO to and from the internal data pool Recognized file extensions: .@ - **vista** a 3d vector field io plugin for vista Recognized file extensions: .V, .VF, .v, .vf Supported element types: floating point 32 bit - **vtk** 3D Vector field in- and output (experimental). No attributes are stored or read. Recognized file extensions: .VTK, .VTKVF, .vtk, .vtkvf Supported element types: floating point 32 bit ## EXAMPLE Transform an image input.v by the transformation defined by the vector field field.v by using bspline interpolation of degree 4 and store the result in output.v mia-3ddeform -i input.v -t field.v -o output.v -p bspline:d=4 ## 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'.