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mia-3dmotioncompica-nonrigid(1) | General Commands Manual | mia-3dmotioncompica-nonrigid(1) |
NAME¶
mia-3dmotioncompica-nonrigid - Non-linear registration of a series of 3D images.
SYNOPSIS¶
mia-3dmotioncompica-nonrigid -i <in-file> -o <out-file> [options]
DESCRIPTION¶
mia-3dmotioncompica-nonrigid This program implements a 3D version of the motion compensation algorithm described in
OPTIONS¶
File-IO¶
- -i --in-file=(input, required); io
- input images of consecutively numbered filed (nameXXXX.ext)
For supported file types see PLUGINS:3dimage/io - -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 - --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'
- --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'
- --save-coeffs=
- save mixing matrix to a text file
- --save-features=
- save feature images as PNG
Help & Info¶
- -V --verbose=warning
- verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:
- --copyright
- print copyright information
- -h --help
- print this help
- -? --usage
- print a short help
- --version
- print the version number and exit
ICA¶
- --fastica=internal
- FastICA implementationto be used
For supported plugins see PLUGINS:fastica/implementation - -C --components=0
- ICA components 0 = automatic estimation
- --no-normalize
- don't normalized ICs
- --no-meanstrip
- don't strip the mean from the mixing curves
- -k --skip=0
- skip images at the beginning of the series e.g. because as they are of other modalities
- -m --max-ica-iter=400
- maximum number of iterations in ICA
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¶
- -O --optimizer=gsl:opt=gd,step=0.1
- Optimizer used for minimization
- -a --start-c-rate=32
- start coefficinet rate in spines, gets divided by --c-rate-divider with every pass
- --c-rate-divider=4
- cofficient rate divider for each pass
- -d --start-divcurl=20
- start divcurl weight, gets divided by --divcurl-divider with every pass
- --divcurl-divider=4
- divcurl weight scaling with each new pass
- -w --imagecost=image:weight=1,cost=ssd,
- image cost
- -l --mg-levels=3
- multi-resolution levels
- -P --passes=3
- registration passes
PLUGINS: 3dimage/io¶
- analyze
- Analyze 7.5 image
- datapool
- Virtual IO to and from the internal data pool
- dicom
- Dicom image series as 3D
- hdf5
- HDF5 3D image IO
- inria
- INRIA image
- mhd
- MetaIO 3D image IO using the VTK implementation (experimental).
- 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.
- vff
- VFF Sun raster format
- vista
- Vista 3D
- vti
- 3D image VTK-XML in- and output (experimental).
- vtk
- 3D VTK image legacy in- and output (experimental).
PLUGINS: fastica/implementation¶
- internal
- This is the MIA implementation of the FastICA algorithm.
- itpp
- This is the IT++ implementation of the FastICA algorithm.
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
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
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'.
v2.4.7 | USER COMMANDS |