Hello,
I found a small bug in recent dev version bin quantifyHAsubregions.sh: leftVolFile="$resultsDirectory/$subjectName/mri/lh.${suffix}Volumes-${suffix}.v20.txt" rightVolFile="$resultsDirectory/$subjectName/mri/rh.${suffix}Volumes-${suffix}.v20.txt"
Should say leftVolFile="$resultsDirectory/$subjectName/mri/lh.${suffix}Volumes-${ *prefix*}.v20.txt" rightVolFile="$resultsDirectory/$subjectName/mri/rh.${suffix}Volumes-${ *prefix*}.v20.txt"
because as specified "T1" is the ${prefix} which is how the subfields file names end. Obviously, can flip suffix and prefix throughout so it is more intuitive. Seems to work fine after this adjustment.
Josh