getfMRInuisanceVariables: Extract generic fMRI nuisance variables for ASL or BOLD

In stnava/itkImageR: Examples using Rcpp to interface R and ITK

Description

Will motion correct, run compcorr and estimate global signal. Outputs a list with the time series data matrix (time by voxels), motion and other nuisance variables, global signal (for BOLD or ASL), the mask and the average time series image. Meant to be used before filterfMRIforNetworkAnalysis or any other results-oriented processing.

Usage

output<-getfMRInuisanceVariables( boldImageOrFileName, maskThresh=100 , moreaccurate=T, mask = myfMRImask )

Arguments

boldImageOrFileName	input antsImage or filename
maskThresh	will use this intensity threshold to estimate a mask otherwise will use the mask passed in
mask	binary image masking the intput image

Value

outputs list described above.

Author(s)

Avants BB

Examples

# set moreaccurate=T for final results 
dd<-getfMRInuisanceVariables( bold, maskThresh=100 , moreaccurate=F )
tsResid<-residuals( lm( dd$matrixTimeSeries ~ dd$globalsignal + dd$nuisancevariables ))
mynetwork<-filterfMRIforNetworkAnalysis( tsResid , tr=4, mask=dd$mask ,cbfnetwork = "BOLD", labels = aalImageLabels , graphdensity = 0.25 )
# use colnames( dd$nuisancevariables ) to see nuisance variables 

ee<-getfMRInuisanceVariables( pcasl, mask = pcaslmask , moreaccurate=F )
tsResid<-residuals( lm( ee$matrixTimeSeries ~ ee$globalsignalASL + ee$nuisancevariables ))
myASLnetwork<-filterfMRIforNetworkAnalysis( tsResid , tr=4, mask=ee$mask ,cbfnetwork = "ASLCBF", labels = aal2asl , graphdensity = 0.25 )
# use colnames( dd$nuisancevariables ) to see nuisance variables 

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