mia-2dmyoica-nonrigid-parallel

Sysnopis:

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

Description:

This program implements the 2D version of the motion compensation algorithm described in Wollny G, Kellman P, Santos A, Ledesma-Carbayo M-J, "Automatic Motion Compensation of Free Breathing acquired Myocardial Perfusion Data by using Independent Component Analysis", Medical Image Analysis, 2012, DOI:10.1016/j.media.2012.02.004.This version of the program may run all registrations in parallel.

Options:

File-IO

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

input perfusion data set

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

output perfusion data set

-r, --registered=reg; stringSTRING

File name base for the registered images. Image type and numbering scheme are taken from the input images as given in the input data set.

--save-cropped=(output); string

save cropped set to this file, the image files will use the stem of the name as file name base

--save-feature=(output); string

save segmentation feature images and initial ICA mixing matrix

--save-refs=(output); string

for each registration pass save the reference images to files with the given name base

--save-regs=(output); string

for each registration pass save intermediate registered images

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
warning:Warnings
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

ICA

-C, --components=0; ulong

ICA components 0 = automatic estimation

--normalize

normalized ICs

--no-meanstrip

don't strip the mean from the mixing curves

-s, --segscale=0; float

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

-k, --skip=0; ulong

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

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

maximum number of iterations in ICA

-E, --segmethod=features; dict

Segmentation method

delta-peak:difference of the peak enhancement images
features:feature images
delta-feature:difference of the feature images
-b, --min-breathing-frequency=-1; float

minimal mean frequency a mixing curve can have to be considered to stem from brething. A healthy rest breating rate is 12 per minute. A negative value disables the test.

Processing

--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).

Registration

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

Optimizer used for minimization. The string value will be used to construct a plug-in.. For supported plug-ins see Plugin type: minimizer/singlecost

-a, --start-c-rate=16; double

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

--c-rate-divider=2; double

Cofficient rate divider for each pass.

-d, --start-divcurl=10000; double

Start divcurl weight, gets divided by --divcurl-divider with every pass.

--divcurl-divider=2; double

Divcurl weight scaling with each new pass.

-w, --imagecost=image:weight=1,cost=ssd; factory

image cost, do not specify the src and ref parameters, these will be set by the program. The string value will be used to construct a plug-in.. For supported plug-ins see Plugin type: 2dimage/fullcost

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

multi-resolution levels

-P, --passes=3; ulong

registration passes

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-nonrigid-parallel   -i segment.set -o registered.set -k 2

Author(s):

Gert Wollny