mia-2dmyoset-all2one-nonrigid {-i string} {-o string} [ options ...] [ Plugin type: 2dimage/fullcost ...]


This program runs non-rigid registration of a series of images given in an image set. All images are registered to one user defined reference image.



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

input perfusion data set

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

output perfusion data set

--out-filebase=reg; stringSTRING

file name basae for registered files, file type is deducted from the image file type in the input data set.


-k, --skip=0; int

Skip images at the beginning of the series

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

Optimizer used for minimization

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

multi-resolution levels

-f, --transForm=spline; factory

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

-r, --ref=-1; int

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

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 in segment.set by optimizing a spline based transformation with a coefficient rate of 16 pixel using Mutual Information and penalize the transformation by using divcurl with aweight of 2.0.

mia-2dmyoset-all2one-nonrigid -i segment.set -o registered.set 
    -f spline:rate=16,penalty=[divcurl:weight=2.0] image:cost=mi,weight=2.0


Gert Wollny