.TH mia\-3dmotioncompica\-nonrigid 1 "v2.4.7" "USER COMMANDS" .SH NAME mia\-3dmotioncompica\-nonrigid \- Non\-linear registration of a series of 3D images. .SH SYNOPSIS .B mia\-3dmotioncompica\-nonrigid \-i \-o [options] .SH DESCRIPTION .B mia\-3dmotioncompica\-nonrigid This program implements a 3D version of the motion compensation algorithm described in .RS .UR https://doi.org/10.1016/j.media.2012.02.004 Wollny G, Kellman P, Santos A, Ledesma-Carbayo M-J, "Automatic Motion Compensation of Free Breathing acquired Myocardial Perfusion Data by using Independent Component Analysis" Medical Image Analysis, 2012 .UE .RE . .SH OPTIONS .SS File-IO .RS .IP "\-i \-\-in-file=(input, required); io" input images of consecutively numbered filed (nameXXXX.ext) For supported file types see PLUGINS:3dimage/io .IP "\-o \-\-out-file=(output, required); io" output image name (as C format string including a %04d in order to define the file numbering) For supported file types see PLUGINS:3dimage/io .IP " \-\-save-refs=" save reference images, the given string is used as file name base, the number pattern follows the input images, and the output format is always 'vista' .IP " \-\-save-regs=" save intermediate registered images, the given string is used as file name base, the number pattern follows the input images, and the output format is always 'vista' .IP " \-\-save-coeffs=" save mixing matrix to a text file .IP " \-\-save-features=" save feature images as PNG .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 trace \(hy Function call trace .RE .RS 10 .I debug \(hy Debug output .RE .RS 10 .I info \(hy Low level messages .RE .RS 10 .I message \(hy Normal messages .RE .RS 10 .I warning \(hy Warnings .RE .RS 10 .I fail \(hy Report test failures .RE .RS 10 .I error \(hy Report errors .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 ICA .RS .IP " \-\-fastica=internal" FastICA implementationto be used For supported plugins see PLUGINS:fastica/implementation .IP "\-C \-\-components=0" ICA components 0 = automatic estimation .IP " \-\-no-normalize" don't normalized ICs .IP " \-\-no-meanstrip" don't strip the mean from the mixing curves .IP "\-k \-\-skip=0" skip images at the beginning of the series e.g. because as they are of other modalities .IP "\-m \-\-max-ica-iter=400" maximum number of iterations in ICA .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 .RS .IP "\-O \-\-optimizer=gsl:opt=gd,step=0.1" Optimizer used for minimization .IP "\-a \-\-start-c-rate=32" start coefficinet rate in spines, gets divided by \-\-c\-rate\-divider with every pass .IP " \-\-c-rate-divider=4" cofficient rate divider for each pass .IP "\-d \-\-start-divcurl=20" start divcurl weight, gets divided by \-\-divcurl\-divider with every pass .IP " \-\-divcurl-divider=4" divcurl weight scaling with each new pass .IP "\-w \-\-imagecost=image:weight=1,cost=ssd," image cost .IP "\-l \-\-mg-levels=3" multi\-resolution levels .IP "\-P \-\-passes=3" registration passes .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. The orientation is transformed in the same way like it is done with 'dicomtonifti --no-reorder' from the vtk-dicom package. .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 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: fastica/implementation .TP 10 .B internal This is the MIA implementation of the FastICA algorithm. .P .RS 14 (no parameters) .RE .TP 10 .B itpp This is the IT++ implementation of the FastICA algorithm. .P .RS 14 (no parameters) .RE .SH EXAMPLE Register the perfusion series given in images imagesXXXX.v by using 4\-class ICA estimation. Skip two images at the beginning, use at most 4 registration threads, a nlopt based optimizer and otherwiese use the default parameters. Store the result in registeredXXXX.v .HP mia\-3dmotioncompica\-nonrigid \-i images0000.v \-o registered%04d.v \-k 2 \-C 4 \-t 4 \-O nlopt:opt=ld\-var1,xtola=0.001,ftolr=0.001,maxiter=300 .SH AUTHOR(s) Gert Wollny .SH COPYRIGHT This software is Copyright (c) 1999\(hy2015 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'.