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 <jgray7...@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
>



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