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


This program runs the image registration of a consecutively numbered image series. The registration is run in a serial manner, this is, only images in temporal succession (i.e. consecutive numbers) are registered, and the obtained transformations are applied accumulated to reach full registration.



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

input perfusion data set

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

file name 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; 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:

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).


Run a serial registration of images inputXXXX.v (X digit) to reference image 20 and store the result in regXXXX.v. Optimize the sum of squared differences and spline transformations with coefficient rate 10.

mia-3dserial-nonrigid -i input0000.v -o 'reg%04d.v' -f spline:rate=10 -r 20 ssd


Gert Wollny