Provided by: mia-tools_2.4.6-1_amd64 
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 series
-e --end=60
last image in series
-C --components=0
nr. 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
--fastica=internal
FastICA implementationto be used
For supported plugins see PLUGINS:fastica/implementation
-x --max-ica-iterations=0
max 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 crop
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).
PLUGINS: 2dimage/io
bmp BMP 2D-image input/output support. The plug-in supports reading and writing of binary images
and 8-bit gray scale images. read-only support is provided for 4-bit gray scale images. The
color table is ignored and the pixel values are taken as literal gray scale values.
('Recognized file extensions: ', '.BMP, .bmp')
Supported element types:
binary data, unsigned 8 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
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 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'.
USER COMMANDS v2.4.6 mia-2dmyocard-ica(1)