mia-2dmyocard-ica(1)

Usage

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

Overview

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=(required, input); 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:

trace ‐ Function call trace

debug ‐ Debug output

info ‐ Low level messages

message ‐ Normal messages

warning ‐ Warnings

fail ‐ Report test failures

error ‐ Report errors

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)

Examples

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

Releases

5 releases since Debian 8 (Jessie); the text changed 3 times.

--fastica since Debian 10 (Buster).

--auto-components until Debian 8 (Jessie); -a until Debian 8 (Jessie).