mia-2dmyocard-ica(1) 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: [email protected]

 
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'.