taskFMRI: Simple taskFMRI function.

Description Usage Arguments Value Author(s) Examples

Description

Input 4D time series matrix. (Perform slice timing correction externally). Estimate hemodynamicRF from block design. Compute brain mask on average bold image. Get nuisance variables : motion , compcor , globalsignal. High-frequency filter the time series ( externally ). Correct for autocorrelation using bullmore 1996 MRM and AR(2) model with parameters derived from global residual signal. Estimate final glm.

Usage

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activationBeta<-taskFMRI(  fmriMatrix , blockDesign )

Arguments

fmriMatrix

input matrix

blockDesign

input array

Value

c( betas ) is output

Author(s)

Avants BB

Examples

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# read the fmri image in and maybe do slice timing correction 
#  fmri<-antsImageRead( fn[2] , 4 )
#  ImageMath(4,fmri,'SliceTimingCorrection',fmri,'bspline')
  myvars<-getfMRInuisanceVariables( fmri, moreaccurate = TRUE ,  maskThresh=100 )
  mat <- timeseries2matrix( fmri, mask )
  mat  <- filterfMRIforNetworkAnalysis( cbind(mat) , 2.5, cbfnetwork = "BOLD" , freqLo=0.001 , freqHi = 0.15  )$filteredTimeSeries
  blockfing = c(0, 36, 72, 108,144)
  hrf <- hemodynamicRF( scans=dim(fmri)[4] , onsets=blockfing , durations=rep(  12,  length( blockfing ) ) ,  rt=2.5 )
  activationBeta<-taskFMRI(  fmriMatrix , hrf , myvars )

stnava/itkImageR documentation built on May 30, 2019, 7:21 p.m.