Hi Pascale,

This is a weird one, particularly since it run the first part, apparently without errors.

Can you please send us:

1. The recon and hippocampal log files.
2. The exact dev version, and information on your system (MAC/Linux, version, etc)

Cheers,

/E

Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

http://www.jeiglesias.com

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Pascale Patenaude <pascalepatenaude@hotmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, March 23, 2020 at 16:55
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Error in segmentation of the hippocampal subfields: /tmp/MCR_3634872073/.mcrCache8.4 error

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Hello FreeSurfer Developers,

I'm attempting to produce an automated segmentation of the hippocampal substructures and the nuclei of the amygdala (see hippocampal module https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala). 

When I try to run the segmentHA_T1.sh SUBJECT_ID  [SUBJECTS_DIR] command with the dev version of freesurfer, I keep getting this error: 

I've tried setting the MCR_CACHE_ROOT env variable to somewhere under my user directory. 

Does anyone have any suggestions on how this can be fixed?

Thank you in advance,

Pascale