--- name: "mia-3dfluid" 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-3dfluid" --- # mia-3dfluid(1) Fluid dynamic 3D registration ## NAME mia-3dfluid - Fluid dynamic 3D registration ## SYNOPSIS **mia-3dfluid -i \ -r \ -o \ \[options\]** ## DESCRIPTION **mia-3dfluid** This program is used for non-rigid registration based on fluid dynamics as described in: Wollny, G. and Kruggel, F., 'Computational cost of non-rigid registration algorithms based on fluid dynamics', IEEE Transactions on Medical Imaging, 11(8), pp. 946-952, 2002. ⟨https://doi.org/10.1109/TMI.2002.803113⟩ It uses SSD as the sole registration criterion. ## OPTIONS ### File-IO - \-i --in-image=(input, required); io input image\ For supported file types see PLUGINS:3dimage/io - \-r --ref-image=(input, required); io reference image \ For supported file types see PLUGINS:3dimage/io - \-o --out-transformation=(output, required); io output transformation comprising the registering transformation field\ For supported file types see PLUGINS:3dtransform/io - \-d --out-image=(output); io save deformed image\ For supported file types see PLUGINS:3dimage/io ### 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). ### Registration parameters - \--disable-multigrid disable multi-grid processing - \--disable-fullres disable processing on the full resolution image - \--lambda=1 elasticy constant - \--mu=1 elasticy constant - \-s --start-size=16 initial multigrided size - \-m --method=sora method for solving PDE *sor* ‐ successive overrelaxation *sora* ‐ Gauss Southwell relexation - \--step=0.8 Initial stepsize - \-p --interpolator=bspline:d=3 image interpolator kernel\ For supported plugins see PLUGINS:1d/splinekernel - \--relax=1 overrelaxation factor vor method sor - \--maxiter=10 maximum iterations - \--epsilon=0.01 truncation condition - \--matter=4 intensity above which real matter is assumed (experimental) ## 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: 3dtransform/io - **bbs** Binary (non-portable) serialized IO of 3D transformations Recognized file extensions: .bbs - **datapool** Virtual IO to and from the internal data pool Recognized file extensions: .@ - **vista** Vista storage of 3D transformations Recognized file extensions: .v, .v3dt - **xml** XML serialized IO of 3D transformations Recognized file extensions: .x3dt ## EXAMPLE Register image test.v to image ref.v and write the deformation vector field regfield.v. Start registration at the smallest size above 16 pixel. mia-3dfluid -i test.v -r ref.v -o regfield.v -s 16 ## 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'.