---
name: "mia-2dmyocard-ica"
section: "1"
platform: "linux"
package: "mia-tools"
version: "2.4.7-11+b1"
release: "Debian 12 (Bookworm)"
platforms: ["linux"]
url: "https://new.carta.tech/mia-2dmyocard-ica"
---

# mia-2dmyocard-ica(1)

Run an ICA analysis on a series of 2D images

## 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

  *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)

## 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'.