mia-2dmyocard-icaseries

NAME

mia-2dmyocard-icaseries - Run an ICA analysis on a series of 2D images

SYNOPSIS

mia-2dmyocard-icaseries -i <in-file> [options]

DESCRIPTION

mia-2dmyocard-icaseries This program is used to run a ICA on a series of myocardial perfusion images given in a segmentation set in order to create sythetic references that can be used for motion correction by image registration. If the aim is to run a full motion compensation then it is better run mia-2dmyoica-nonrigid, since this program is essentially the same without the registration bits.

OPTIONS

File-IO

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

input perfusion data set

-r --references=(output); string

File name base for the reference images. Image type and numbering scheme are taken from the input images.

-c --save-cropped=(output); string

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

--save-feature=(output); string

save the features images resulting from the ICA and some intermediate images used for the RV-LV segmentation with the given file name base to PNG files. Also save the coefficients of the initial best and the final IC mixing matrix.

Help & Info

-V --verbose=warning

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace - Function call trace
debug - Debug output
info - Low level messages
message - Normal messages
warning - Warnings
fail - Report test failures
error - Report errors
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

ICA

--fastica=internal

FastICA implementationto be used
For supported plugins see PLUGINS:fastica/implementation

-C --components=0

ICA components 0 = automatic estimation

--normalize

normalized ICs

--no-meanstrip

don’t strip the mean from the mixing curves

-s --segscale=1.4

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

-k --skip=0

skip images at the beginning of the series as they are of other modalities

-m --max-ica-iter=400

maximum number of iterations in ICA

-E --segmethod=features

Segmentation method

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

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).

PLUGINS: fastica/implementation

internal

This is the MIA implementation of the FastICA algorithm.

(no parameters)

itpp

This is the IT++ implementation of the FastICA algorithm.

(no parameters)

EXAMPLE

Evaluate the synthetic references from set segment.set and save them to refXXXX.??? by using five independend components, and skipping 2 images. Per default a bounding box around the LV will be segmented and scaled by 1.4 and the cropped images will be saved to cropXXXX.??? and a segmentation set cropped.set is created. The image file type ??? is deducted from the input images in segment.set.

mia-2dmyocard-icaseries -i segment.set -r ref -o ref -k 2 -C 5

AUTHOR(s)

Gert Wollny

COPYRIGHT

This software is Copyright (c) 1999-2015 Leipzig, Germany and Madrid, Spain. It comes with ABSOLUTELY NO WARRANTY and you may redistribute it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 (or later). For more information run the program with the option ’--copyright’.