Provided by: mia-tools_2.2.7-3_amd64 
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, DOI:10.1016/j.media.2012.02.004.
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:
info ‐ Low level messages
trace ‐ Function call trace
fail ‐ Report test failures
warning ‐ Warnings
error ‐ Report errors
debug ‐ Debug output
message ‐ Normal messages
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
-C --components=0
ICA components 0 = automatic estimationICA 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 modalitiesskip
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 ICAmaximum 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).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 passstart
coefficinet rate in spines, gets divided by --c-rate-divider with every pass
--c-rate-divider=4
cofficient rate divider for each passcofficient rate divider for each pass
-d --start-divcurl=20
start divcurl weight, gets divided by --divcurl-divider with every passstart divcurl
weight, gets divided by --divcurl-divider with every pass
--divcurl-divider=4
divcurl weight scaling with each new passdivcurl weight scaling with each new pass
-w --imagecost=image:weight=1,cost=ssd,
image cost
-l --mg-levels=3
multi-resolution levelsmulti-resolution levels
-P --passes=3
registration passesregistration 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
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:
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
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'.
USER COMMANDS v2.2.7 mia-3dmotioncompica-nonrigid(1)