mia-2dmyoica-nonrigid-parallel {-i string} {-o string} [ options ...]


This program implements the 2D 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.This version of the program may run all registrations in parallel.



-i, --in-file=(input, required); string

input perfusion data set

-o, --out-file=(output, required); string

output perfusion data set

-r, --registered=reg; stringSTRING

File name base for the registered images. Image type and numbering scheme are taken from the input images as given in the input data set.

--save-cropped=(output); string

save cropped set to this file, the image files will use the stem of the name as file name base

--save-feature=(output); string

save segmentation feature images and initial ICA mixing matrix

--save-refs=(output); string

for each registration pass save the reference images to files with the given name base

--save-regs=(output); string

for each registration pass save intermediate registered images

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
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


-C, --components=0; ulong

ICA components 0 = automatic estimation


normalized ICs


don't strip the mean from the mixing curves

-s, --segscale=0; float

segment and scale the crop box around the LV (0=no segmentation)

-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

-E, --segmethod=features; dict

Segmentation method

delta-peak:difference of the peak enhancement images
features:feature images
delta-feature:difference of the feature images
-b, --min-breathing-frequency=-1; float

minimal mean frequency a mixing curve can have to be considered to stem from brething. A healthy rest breating rate is 12 per minute. A negative value disables the test.


--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).


-O, --optimizer=gsl:opt=gd,step=0.1; factory

Optimizer used for minimization. The string value will be used to construct a plug-in.. For supported plug-ins see Plugin type: minimizer/singlecost

-a, --start-c-rate=16; double

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

--c-rate-divider=2; double

Cofficient rate divider for each pass.

-d, --start-divcurl=10000; double

Start divcurl weight, gets divided by --divcurl-divider with every pass.

--divcurl-divider=2; double

Divcurl weight scaling with each new pass.

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

image cost, do not specify the src and ref parameters, these will be set by the program. The string value will be used to construct a plug-in.. For supported plug-ins see Plugin type: 2dimage/fullcost

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

multi-resolution levels

-P, --passes=3; ulong

registration passes


Register the perfusion series given in 'segment.set' by using automatic ICA estimation. Skip two images at the beginning and otherwiese use the default parameters. Store the result in 'registered.set'.

mia-2dmyoica-nonrigid-parallel   -i segment.set -o registered.set -k 2


Gert Wollny