xenial (1) mia-2dmyocard-icaseries.1.gz
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=(input, required); 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:
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
ICA
-C --components=0
ICA components 0 = automatic estimationICA 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)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 modalitiesskip images at
the beginning of the series as they are of other modalities
-m --max-ica-iter=400
maximum number of iterations in ICAmaximum 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
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).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
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'.