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
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 ⟨https://doi.org/10.1016/j.media.2012.02.004⟩
OPTIONS
File-IO
- -i --in-file=(required, input); io
-
input images of consecutively numbered filed (nameXXXX.ext)
For supported file types see PLUGINS:3dimage/io
- -o --out-file=(required, output); 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:
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
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
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: fastica/implementation
- internal
-
This is the MIA implementation of the FastICA algorithm.
(no parameters)
- itpp
-
This is the IT++ implementation of the FastICA algorithm.
(no parameters)
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'.