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To whom it may concern,

I am attempting to run the hippocampal and amygdala segmentation 
 on the development version of FreeSurfer. However, I am running into a couple 
errors when running the segmentHA_T1.sh script.

The first error is that the script is looking for 
segmentSubjectT1_autoEstimateAlveusML in the wrong directory. It is currently 
looking for this command in /usr/local/freesurfer/bin/ however I need to change 
this path to /g5/dcn/freesurfer_testing/HippoSegment_Test/freesurfer/bin/. I 
couldn't find where to change this path in 
run_segmentSubjectT1_autoEstimateAlveusML.sh. Where is this path defined so I 
can change it?

Secondly, the error output states that I am missing the following files in the 
subject's mri folder:
I believe these files are created using recon-all -all -s [subjectname]. I ran 
this command before segmentHA_T1.sh using MPRAGE dicoms, and it seemed to have 
run without noticeable error, but these four files are still missing. How would 
I go about resolving this to create these files?

Thank you in advance for the help!



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