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.
input images of consecutively numbered filed (nameXXXX.ext). For supported file types see Plugin type: 3dimage/io
output image name (as C format string including a %04d in order to define the file numbering). For supported file types see Plugin type: 3dimage/io
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 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 mixing matrix to a text file
save feature images as PNG
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|
|fatal:||Report only fatal errors|
print copyright information
print this help
print a short help
print the version number and exit
ICA components 0 = automatic estimation
don't normalized ICs
don't strip the mean from the mixing curves
skip images at the beginning of the series e.g. because as they are of other modalities
maximum number of iterations in ICA
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).
Optimizer used for minimization
start coefficinet rate in spines, gets divided by --c-rate-divider with every pass
cofficient rate divider for each pass
start divcurl weight, gets divided by --divcurl-divider with every pass
divcurl weight scaling with each new pass
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