filterfMRIforNetworkAnalysis: Basic pre-processing for BOLD or ASL-based network analysis.
In stnava/itkImageR: Examples using Rcpp to interface R and ITK

Description Usage Arguments Value Author(s) Examples

This function works for either raw BOLD time-series data, ASL-based BOLD time-series data or ASL-based CBF time series data. In all 3 cases, this function performs motion-correction, factoring out motion and compcor nuisance paramters, frequency filtering and masking. The output contains the filtered time series (matrix form), the mask and a vector of temporal signal variance. Some ASL MR sequences allow network analysis of either BOLD or ASL signal. See "Implementation of Quantitative Perfusion Imaging Techniques for Functional Brain Mapping using Pulsed Arterial Spin Labeling" by Wong et al, 1997 for an overview. This function employs "surround" techniques for deriving either CBF or BOLD signal from the input ASL. This is a WIP.

1	filterfMRIforNetworkAnalysis( asl_antsr_image_or_filename, tr, freqLo=0.01, freqHi = 0.1, cbfnetwork=c("BOLD", "ASLBOLD", "ASLCBF") , maskThresh=500, smoother = 0, outputprefix = NULL )

`asl_antsr_image_or_filename`	The filename to an antsr image or pointer to an antsr image
`tr = <value>`	The sequence's TR value , typically 3 or 4.
`freqLo = <value>`	The lower frequency limit, e.g. 0.01 in band-pass filter
`freqHi = <value>`	The higher frequency limit, e.g. 0.1 in band-pass filter
`cbfnetwork = "ASLCBF"`	A string dictating whether to do nothing special (standard BOLD) or get CBF (ASLCBF) or BOLD (ASLBOLD) signal from ASL
`maskThresh = <value>`	A thresholding value for the mask ... may need to be adjusted up or down for your data although the mask does not need to be perfect.
`smoother = <value>`	A smoothing parameter for space and time.
`outputprefix = <string>`	filename prefix - if defined , this function will write out some sanity checking images.

output is a list containing "filteredTimeSeries" "mask" "temporalvar"

1 – Failure

Avants BB

## Not run: 
fmat<-timeseries2matrix( img, mask )
myres<-filterfMRIforNetworkAnalysis(fmat,tr=4,0.01,0.1,cbfnetwork="BOLD", mask = mask )

## End(Not run)