| mia-2dmyocard-ica(1) | General Commands Manual | mia-2dmyocard-ica(1) |
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=(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
- -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:
- --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.
- datapool
- Virtual IO to and from the internal data pool
- dicom
- 2D image io for DICOM
- exr
- a 2dimage io plugin for OpenEXR images
- jpg
- a 2dimage io plugin for jpeg gray scale images
- png
- a 2dimage io plugin for png images
- raw
- RAW 2D-image output support
- tif
- TIFF 2D-image input/output support
- vista
- a 2dimage io plugin for vista images
PLUGINS: fastica/implementation¶
- internal
- This is the MIA implementation of the FastICA algorithm.
- itpp
- This is the IT++ implementation of the FastICA algorithm.
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'.
| v2.4.7 | USER COMMANDS |