ANTsR (version 0.3.3)

getfMRInuisanceVariables: Extract generic fMRI nuisance variables for ASL or BOLD

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

getfMRInuisanceVariables(fmri, maskThresh = 500, moreaccurate = 1, mask = NA)

Arguments

fmri

input antsImage or filename

maskThresh

will use this intensity threshold to estimate a mask otherwise will use the mask passed in

moreaccurate

zero, one or two with increasing accuracy/computation

mask

binary image masking the intput image, precedent over mask thresh

Value

outputs list described above.

Examples

## Not run: 
# if (!exists("fn") ) fn<-getANTsRData("pcasl")
# pcasl<-antsImageRead( fn )
# aslmean<-getAverageOfTimeSeries( pcasl )
# aslmask<-getMask(aslmean)
# ee<-getfMRInuisanceVariables( pcasl, mask = aslmask ,
#         moreaccurate=F )
# ## End(Not run)