mia-3dmotioncompica-nonrigid

Sysnopis:

mia-3dmotioncompica-nonrigid {-i io} {-o io} [ options ...]

Description:

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 Plugin type: 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 Plugin type: 3dimage/io

--save-refs=STRING

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=STRING

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=STRING

save mixing matrix to a text file

--save-features=STRING

save feature images as PNG

Help & Info

-V, --verbose=warning; dict

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=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

ICA

-C, --components=0; ulong

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; ulong

skip images at the beginning of the series e.g. because as they are of other modalities

-m, --max-ica-iter=400; ulong

maximum number of iterations in ICA

Processing

--threads=-1; int

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; stringSTRING

Optimizer used for minimization

-a, --start-c-rate=32; double

start coefficinet rate in spines, gets divided by --c-rate-divider with every pass

--c-rate-divider=4; double

cofficient rate divider for each pass

-d, --start-divcurl=20; double

start divcurl weight, gets divided by --divcurl-divider with every pass

--divcurl-divider=4; double

divcurl weight scaling with each new pass

-w, --imagecost=image:weight=1,cost=ssd,; stringSTRING

image cost

-l, --mg-levels=3; ulong

multi-resolution levels

-P, --passes=3; ulong

registration passes

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