mia-2dgroundtruthreg {-i string} {-o string} {-A double} {-B double} {-R double} [ options ...]


This program implements the non-linear registration based on Pseudo Ground Thruth for motion compensation of series of myocardial perfusion images as described in

Chao Li and Ying Sun, 'Nonrigid Registration of Myocardial Perfusion MRI Using Pseudo Ground Truth' , In Proc. Medical Image Computing and Computer-Assisted Intervention MICCAI 2009, 165-172, 2009.

Note that for this nonlinear motion correction a preceding linear registration step is usually required.



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

input perfusion data set

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

output perfusion data set

-r, --registered=reg; stringSTRING

file name base for registered files


-s, --skip=2; ulong

skip images at beginning of series

-P, --passes=4; ulong

number of registration passes


-A, --alpha=(required); double

spacial neighborhood penalty weight

-B, --beta=(required); double

temporal second derivative penalty weight

-R, --rho_thresh=(required); double

correlation threshold for neighborhood analysis


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

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

-p, --interpolator=bspline:d=3; factory

image interpolator kernel. For supported plug-ins see Plugin type: 1d/splinekernel

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

multi-resolution levels

-d, --divcurl=20; double

divcurl regularization weight

--divcurl-divider=4; double

divcurl weight scaling with each new pass

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

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

-w, --imageweight=1; double

image cost weight

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

debug:Debug output
message:Normal messages
info:Low level messages
error:Report errors
fatal:Report only fatal errors
trace:Function call trace
fail:Report test failures
--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 by images imageXXXX.exr by using Pseudo Ground Truth estimation. Skip two images at the beginning and otherwiese use the default parameters. Store the result images to 'regXXXX.exr'.

mia-2dgroundtruthreg -i imageXXXX.exr -o regXXXX.exr -k 2


Gert Wollny