Hi Pascale,

 

Yes, it’d be very helpful to know what OS and version you are running on. So, when you set MCR_CACHE_ROOT to somewhere other than /tmp, you still get the same failbit error, right? Can you run this again with MCR_CACHE_ROOT pointing to your user dir, then try running the referenced kvlSetMeshCollectionPostions.m file independently? I think it’d be helpful to see the output from this test.

 

Also, were you able to fix the GLIBCXX_3.4.19 errors that you found previously?

 

best

Andrew

 

 

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ@mgh.harvard.edu>
Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, March 23, 2020 at 5:56 PM
To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Error in segmentation of the hippocampal subfields: /tmp/MCR_3634872073/.mcrCache8.4 error

 

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

 

        External Email - Use Caution        

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: 

 

cid:image001.png@01D6013C.206E3F90

 

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