Re: [Freesurfer] Error in segmentation of the hippocampal subfields: /tmp/MCR_3634872073/.mcrCache8.4 error

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/HippocampalSubfieldsAndNucleiOfAmy...).

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