mia-3dmany2one-nonrigid {-i io} [ options ...] [ Plugin type: 3dimage/fullcost ...]


This program runs the non-rigid registration of an image series by registereing all images to a user-selected reference.



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

input perfusion data set. For supported file types see Plugin type: 3dimage/io

-o, --out-file=(output); io

file name for registered files. For supported file types see Plugin type: 3dimage/io


-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: 3dimage/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:

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 images given as numbered files imagesXXXX.v by optimizing a spline based transformation with a coefficient rate of 16 pixel using a weighted combination of normalized gradient fields and SSD as cost measure, and penalize the transformation by using divcurl with aweight of 2.0. Store the resultsing images in registeredXXXX.v.

mia-3dmany2one-nonrigid -i images0000.v -o  registered%04d.v -F spline:rate=16 image:cost=[ngf:eval=ds],weight=2.0 image:cost=ssd,weight=0.1 divcurl:weight=2.0


Gert Wollny