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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 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. 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:
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'.
v2.4.3 USER COMMANDS