mia-2dmyoserial-nonrigid

Sysnopis:

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

Description:

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,

Options:

File-IO

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

input perfusion data set

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

output perfusion data set

-R, --registered=reg

file name base for registered fiels

Registration

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

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

-l, --mg-levels=3

multi-resolution levels

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

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

-r, --ref=-1

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

-k, --skip=0

skip registration of these images at the beginning of the series

Help & Info

-V, --verbose=warning

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
warning:Warnings
error:Report errors
debug:Debug output
message:Normal messages
fatal:Report only fatal errors
--copyright

print copyright information

-h, --help

print this help

-?, --usage

print a short help

--version

print the version number and exit

Processing

--threads=-1

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).

Example:

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]

Author(s):

Gert Wollny