mia-2dmyoica-nonrigid2

Sysnopis:

mia-2dmyoica-nonrigid2 {-i string} {-o string} [ options ...]

Description:

This program runs the non-rigid registration of an perfusion image series.In each pass, first an ICA analysis is run to estimate and eliminate the periodic movement and create reference images with intensities similar to the corresponding original image. Then non-rigid registration is run using the an "ssd + divcurl" cost model. The B-spline c-rate and the divcurl cost weight are changed in each pass according to given parameters.In the first pass a bounding box around the LV myocardium may be extractedto speed up computation Special note to this implemnentation: the registration is always run from the original images to avoid the accumulation of interpolation errors.

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

--save-cropped=STRING

save cropped set to this file

--save-feature=STRING

save segmentation feature images and initial ICA mixing matrix

ICA

-C, --components=0

ICA components 0 = automatic estimation

--normalize

don't normalized ICs

--no-meanstrip

don't strip the mean from the mixing curves

-s, --segscale=0

segment and scale the crop box around the LV (0=no segmentation)

-k, --skip=0

skip images at the beginning of the series e.g. because as they are of other modalities

-m, --max-ica-iter=400

maximum number of iterations in ICA

-E, --segmethod=features

Segmentation method

delta-peak:difference of the peak enhancement images
features:feature images
delta-feature:difference of the feature images

Registration

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

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

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

start coefficinet rate in spines, gets divided by --c-rate-divider with every pass

--c-rate-divider=4

cofficient rate divider for each pass

-d, --start-divcurl=20

start divcurl weight, gets divided by --divcurl-divider with every pass

--divcurl-divider=4

divcurl weight scaling with each new pass

-w, --imageweight=1

image cost weight

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

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

-l, --mg-levels=3

multi-resolution levels

-P, --passes=3

registration passes

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' by using automatic ICA estimation. Skip two images at the beginning and otherwiese use the default parameters. Store the result in 'registered.set'.

mia-2dmyoica-nonrigid2   -i segment.set -o registered.set -k 2

Author(s):

Gert Wollny