.TH mia\-3dfluid 1 "17 October 2014" "2.0.10" "USER COMMANDS" .SH NAME mia\-3dfluid \- Fluid dynamic 3D registration .SH SYNOPSIS .B mia\-3dfluid \-i \-r \-o [options] .SH DESCRIPTION .B 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, doi:10.1109/TMI.2002.803113. It uses SSD as the sole registration criterion. .SH OPTIONS .SS File-IO .RS .IP "\-i \-\-in-image=(input,required)" input image For supported file types see PLUGINS:3dimage/io .IP "\-r \-\-ref-image=(input,required)" reference image For supported file types see PLUGINS:3dimage/io .IP "\-o \-\-out-deformation=(output,required)" output vector field For supported file types see PLUGINS:3dtransform/io .IP "\-d \-\-deformed-image=(output)" save deformed image For supported file types see PLUGINS:3dimage/io .RE .SS Help & Info .RS .IP "\-V \-\-verbose=warning" verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are: .RS 10 .I info \(hy Low level messages .RE .RS 10 .I trace \(hy Function call trace .RE .RS 10 .I fail \(hy Report test failures .RE .RS 10 .I warning \(hy Warnings .RE .RS 10 .I error \(hy Report errors .RE .RS 10 .I debug \(hy Debug output .RE .RS 10 .I message \(hy Normal messages .RE .RS 10 .I fatal \(hy Report only fatal errors .RE .IP " \-\-copyright" print copyright information .IP "\-h \-\-help" print this help .IP "\-? \-\-usage" print a short help .IP " \-\-version" print the version number and exit .RE .SS Processing .RS .IP " \-\-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). .RE .SS Registration parameters .RS .IP " \-\-disable-multigrid" disable multi\-grid processing .IP " \-\-disable-fullres" disable processing on the full resolution image .IP " \-\-lambda=1" elasticy constant .IP " \-\-mu=1" elasticy constant .IP "\-s \-\-start-size=16" initial multigrided size .IP "\-m \-\-method=sora" method for solving PDE .RS 10 .I sor \(hy succesive overrelaxation .RE .RS 10 .I sora \(hy Gauss Southwell relexation .RE .IP " \-\-step=0.8" Initial stepsize .IP "\-p \-\-interpolator=bspline:d=3" image interpolator kernel For supported plugins see PLUGINS:1d/splinekernel .IP " \-\-relax=1" overrelaxation factor vor method sor .IP " \-\-maxiter=10" maxium iterations .IP " \-\-epsilon=0.01" truncation condition .IP " \-\-matter=4" intensity above which real matter is assumed (experimental) .RE .SH PLUGINS: 1d/splinekernel .TP 10 .B bspline B-spline kernel creation , supported parameters are: .P .RS 14 .I d = 3 (int) .RS 2 Spline degree. in [0, 5] .RE .RE .TP 10 .B omoms OMoms-spline kernel creation, supported parameters are: .P .RS 14 .I d = 3 (int) .RS 2 Spline degree. in [3, 3] .RE .RE .SH PLUGINS: 3dimage/io .TP 10 .B analyze Analyze 7.5 image .P .RS 14 Recognized file extensions: .HDR, .hdr .RE .RS 14 Supported element types: .RS 2 unsigned 8 bit, signed 16 bit, signed 32 bit, floating point 32 bit, floating point 64 bit .RE .RE .TP 10 .B datapool Virtual IO to and from the internal data pool .P .RS 14 Recognized file extensions: .@ .RE .TP 10 .B dicom Dicom image series as 3D .P .RS 14 Recognized file extensions: .DCM, .dcm .RE .RS 14 Supported element types: .RS 2 signed 16 bit, unsigned 16 bit .RE .RE .TP 10 .B hdf5 HDF5 3D image IO .P .RS 14 Recognized file extensions: .H5, .h5 .RE .RS 14 Supported element types: .RS 2 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 .RE .RE .TP 10 .B inria INRIA image .P .RS 14 Recognized file extensions: .INR, .inr .RE .RS 14 Supported element types: .RS 2 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 .RE .RE .TP 10 .B mhd MetaIO 3D image IO using the VTK implementation (experimental). .P .RS 14 Recognized file extensions: .MHA, .MHD, .mha, .mhd .RE .RS 14 Supported element types: .RS 2 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 .RE .RE .TP 10 .B nifti NIFTI-1 3D image IO .P .RS 14 Recognized file extensions: .NII, .nii .RE .RS 14 Supported element types: .RS 2 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 .RE .RE .TP 10 .B vff VFF Sun raster format .P .RS 14 Recognized file extensions: .VFF, .vff .RE .RS 14 Supported element types: .RS 2 unsigned 8 bit, signed 16 bit .RE .RE .TP 10 .B vista Vista 3D .P .RS 14 Recognized file extensions: .V, .VISTA, .v, .vista .RE .RS 14 Supported element types: .RS 2 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 .RE .RE .TP 10 .B vti 3D image VTK-XML in- and output (experimental). .P .RS 14 Recognized file extensions: .VTI, .vti .RE .RS 14 Supported element types: .RS 2 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 .RE .RE .TP 10 .B vtk 3D VTK image legacy in- and output (experimental). .P .RS 14 Recognized file extensions: .VTK, .VTKIMAGE, .vtk, .vtkimage .RE .RS 14 Supported element types: .RS 2 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 .RE .RE .SH PLUGINS: 3dtransform/io .TP 10 .B bbs Binary (non-portable) serialized IO of 3D transformations .P .RS 14 Recognized file extensions: .bbs .RE .TP 10 .B datapool Virtual IO to and from the internal data pool .P .RS 14 Recognized file extensions: .@ .RE .TP 10 .B vista Vista storage of 3D transformations .P .RS 14 Recognized file extensions: .v, .v3dt .RE .TP 10 .B xml XML serialized IO of 3D transformations .P .RS 14 Recognized file extensions: .x3dt .RE .SH 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. .HP mia\-3dfluid \-i test.v \-r ref.v \-o regfield.v \-s 16 .SH AUTHOR(s) Gert Wollny .SH COPYRIGHT This software is Copyright (c) 1999\(hy2013 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'.