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To whom it may concern,

 

I am attempting to run the hippocampal and amygdala segmentation (https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala) 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:

lh.hippoSfVolumes-T1.v21.txt

lh.amygNucVolumes-T1.v21.txt

rh.hippoSfVolumes-T1.v21.txt

rh.amygNucVolumes-T1.v21.txt

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!

 

Best,

CC

 

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