mia-2dmyoserial-nonrigid {-i string} {-o string} [ options ...] [ Plugin type: 2dimage/fullcost ...]


This program runs the non-rigid motion compensation registration of an perfusion image series. The registration is run in a serial manner, this is, only images in temporal succession are registered, and the obtained transformations are applied accumulated to reach full registration. See e.g. Wollny, G., Ledesma-Carbayo, M.J., Kellman, P., Santos, A. "A New Similarity Measure for Non-Rigid Breathing Motion Compensation of Myocardial Perfusion MRI ". Proc 30th Annual International IEEE EMBS Conference, pp. 3389-3392. Vancouver, Aug. 2008, doi:10.1109/IEMBS.2008.4649933,



-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


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

Optimizer used for minimization. For supported plug-ins see Plugin type: minimizer/singlecost

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

multi-resolution levels

-f, --transForm=spline:rate=16,penalty=[divcurl:weight=0.01]; factory

transformation type. For supported plug-ins see Plugin type: 2dimage/transform

-r, --ref=-1; int

reference frame (-1 == use image in the middle)

-k, --skip=0; int

skip registration of these images at the beginning of the series

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


--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).


Register the perfusion series given in 'segment.set' to reference image 30. Skip two images at the beginning and using mutual information as cost function, and penalize the transformation by divcurl with weight 5. Store the result in 'registered.set'.

mia-2dmyoserial-nonrigid   -i segment.set -o registered.set -k 2  -r 30 image:cost=mi -f spline:rate=5,penalty=[divcurl:weight=5]


Gert Wollny