Realized in my tooling around I had flipped T1 and hippoSf in my command. Here is how the adjustment needs to be made for:

quantifyHAsubregions.sh hippoSf <T1>-<analysisID> <output_file> <OPTIONAL_SUBJECTS_DIR>

leftVolFile="$resultsDirectory/$subjectName/mri/lh.${*prefix*}Volumes-${*suffix*}.v20.txt" rightVolFile="$resultsDirectory/$subjectName/mri/rh.${*prefix*}Volumes-${*suffix*}.v20.txt"

On Tue, Sep 19, 2017 at 9:23 AM, Josh Gray jgray7700@gmail.com wrote:

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

Joshua C. Gray, PhD Psychology Instructor Center for Deployment Psychology Work: (301) 816-4768 www.deploymentpsych.org