mia-2dmyocard-icaseries(1)

Usage

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

Overview

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)

Examples

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

Releases

5 releases since Debian 8 (Jessie); the text changed 3 times.

--fastica since Debian 10 (Buster).