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PROGRAM:

NAME


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

SYNOPSIS


mia-2dmyocard-ica -i <in-base> [options]

DESCRIPTION


mia-2dmyocard-ica This program is used to run a ICA on a series of myocardial perfusion
images 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 to create
a segmentation set and use mia-2dmyoica-nonrigid. If the input data is given by means of a
segmentation set, then on can also use mia-2dmyocard-icaseries. This program is
essentially used to test different options on how to run the ICA forreference image
creation.

OPTIONS


-i --in-base=(input, required); io
input file name ofolloing pattern nameXXXX.ext X=numbers For supported file
types see PLUGINS:2dimage/io

--coefs=
output mixing coefficients to this file

-o --out-base=(output); string
output file name base

-t --type=exr
output file type
Supported values are:( @, BMP, DCM, EXR, JPEG, JPG, PNG, RAW,
TIF, TIFF, V, VISTA, bmp, dcm, exr, jpeg, jpg, png, raw, tif,
tiff, v, vista, )

-k --skip=2
skip images at beginning of seriesskip images at beginning of series

-e --end=60
last image in serieslast image in series

-C --components=0
nr. of components, 0=estimate automaticallynr. of components, 0=estimate
automatically

-m --strip-mean
strip mean image from series

-f --save-features=
save feature image

-p --strip-periodic
strip only periodic component

-x --max-ica-iterations=0
max ICA solver iterationsmax ICA solver iterations

-n --ica-normalize
ica_normalize feature images

--all-features=
save all feature images to

-L --LV-crop-amp=0
LV crop mask amplification, 0.0 = don't cropLV crop mask amplification, 0.0
= don't crop

-a --auto-components
automatic esitmation of number of components based on correlation. Implies
-m and -n (Experimental)

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

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).

PLUGINS: 2dimage/io


bmp BMP 2D-image input/output support

Recognized file extensions: .BMP, .bmp

Supported element types:
binary data, unsigned 8 bit, unsigned 16 bit

datapool Virtual IO to and from the internal data pool

Recognized file extensions: .@

dicom 2D image io for DICOM

Recognized file extensions: .DCM, .dcm

Supported element types:
signed 16 bit, unsigned 16 bit

exr a 2dimage io plugin for OpenEXR images

Recognized file extensions: .EXR, .exr

Supported element types:
unsigned 32 bit, floating point 32 bit

jpg a 2dimage io plugin for jpeg gray scale images

Recognized file extensions: .JPEG, .JPG, .jpeg, .jpg

Supported element types:
unsigned 8 bit

png a 2dimage io plugin for png images

Recognized file extensions: .PNG, .png

Supported element types:
binary data, unsigned 8 bit, unsigned 16 bit

raw RAW 2D-image output support

Recognized file extensions: .RAW, .raw

Supported element types:
binary data, signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit,
signed 32 bit, unsigned 32 bit, floating point 32 bit, floating point 64
bit

tif TIFF 2D-image input/output support

Recognized file extensions: .TIF, .TIFF, .tif, .tiff

Supported element types:
binary data, unsigned 8 bit, unsigned 16 bit, unsigned 32 bit

vista a 2dimage io plugin for vista images

Recognized file extensions: .V, .VISTA, .v, .vista

Supported element types:
binary data, signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit,
signed 32 bit, unsigned 32 bit, floating point 32 bit, floating point 64
bit

EXAMPLE


Evaluate the synthetic references from images imageXXXX.exr and save them to refXXXX.exr
by using five independend components, mean stripping, normalizing, and skipping 2 images.

mia-2dmyocard-ica -i imageXXXX.exr -o ref -k 2 -C 5 -m -n

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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