mia-3dmotioncompica-nonrigid(1)
3dmotioncompica-nonrigid
Description
mia-3dmotioncompica-nonrigid
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=(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’.