xenial (1) mia-2dmyocard-ica.1.gz

Provided by: mia-tools_2.2.7-3_amd64 bug

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 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:  .@

       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

       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'.