ANTsR (version 1.0)

antsSpatialICAfMRI: Perform spatial ICA on fMRI bold data.

Description

Perform spatial ICA on group or individual fMRI data. Preprocessing should be performed prior to calling this function (cf antsPreprocessfMRI.R).

Usage

antsSpatialICAfMRI <- function( boldImages, maskImage = NA, numberOfICAComponents = 20,
  normalizeComponentImages = TRUE )

Arguments

boldImages

a list of 4-D ANTs image fMRI data.

maskImage

A 3-D ANTs image defining the region of interest. This must be specified.

numberOfICAComponents

Number of estimated observers (components).

normalizeComponentImages

Boolean to specify whether each component vector element is normalized to its z-score.

Value

Output list includes standard ICA matrices from the fastICA algorithm:

X = pre-processed data matrix

K = pre-whitening matrix that projects data onto the first n.comp principal components

W = estimated un-mixing matrix (see definition in details)

A = estimated mixing matrix

S = estimated source matrix

and the component images.

Examples

# NOT RUN {
boldImages <- list()
boldImages[[1]] <- antsImageRead( "subject1.nii.gz", dim = 4, pixeltype = "float" )
boldImages[[2]] <- antsImageRead( "subject2.nii.gz", dim = 4, pixeltype = "float" )
boldImages[[3]] <- antsImageRead( "subject3.nii.gz", dim = 4, pixeltype = "float" )
boldImages[[4]] <- antsImageRead( "subject4.nii.gz", dim = 4, pixeltype = "float" )

maskImage <- NA

cleanBoldImages <- list()
for( i in 1:length( boldImages[[1]] ) )
  {
  fmri <- antsPreprocessfMRI( boldImages[[i]] )
  if( i == 1 )
    {
    maskImage <- fmri$maskImage
    }
  cleanBoldImages[[i]] <- fmri$cleanBoldImage
  }

icaResults <- antsSpatialICAfMRI( cleanBoldImages, numberOfICAComponents = 20, cleanBoldImages[[i]] )
componentImages <- icaResults$componentImages

# write out the component images
for( i in 1:length( icaResults$componentImages ) )
  {
  componentFileName <- paste0( "componentImage", i, ".nii.gz" )
  cat( "Writing ", componentFileName, ".\n" )
  antsImageWrite( componentImages[[i]], componentFileName )
  }
# }