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'.