(C) Michael Perry, Stanford University [2012-2014]
####pitt_initData
This will organize all the data into the format we prefer
####pitt_initAnatomicals
This will convert the anatomical images to nifti format and run mrAnatAverageAcpcNifti Could also run freesurfer segmentation at this point. Those ROIS will need to be converted to nifti or mat for use with various tools. The ROI toolbox will be important for this.
####pitt_segmentAnatomicals
This will segment the anatomical files using freesurfer and convert the ROIs to individual nifti files (this is what dtiRoiFromNifti was written for)
####pitt_preprocessDiffusion
This will convert the raw scanner data to nifti and process the data using MRD.
####pitt_fiberTracker
This will allow any two rois to be used to track fibers. either using contrack or stt ADD this as an option on the pittdti gui - the idea being that the user could choose do do this kind of fiber tracking from the gui and close the gui (or leave it open)
####pitt_fiberTrackMoriGroups
This will track the mori groups for each subject
####pitt_getStats
Get and display stats for a given fiber group(s).