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PROGRAM:

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'.

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