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


This program implements 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.



-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 registered fiels


save cropped set to this file


save the features images resulting from the ICA and some intermediate images used for the RV-LV segmentation with the given file name base to PNG files. Also save the coefficients of the initial best and the final IC mixing matrix.


save synthetic reference images


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. For supported plug-ins see Plugin type: minimizer/singlecost

-R, --refiner=

optimizer used for refinement after the main optimizer was called. 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=10; 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. For supported plug-ins see Plugin type: 2dimage/fullcost

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

multi-resolution levels

-P, --passes=5; 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   -i segment.set -o registered.set -k 2


Gert Wollny