Hi Andrew and Juan,

Thanks so much for your help! Pascale was able to get some subjects run without error but some failed with the "/tmp/MCR_ ...." error. Not sure why it is happening intermittently. Some of these subjects' recon-all was done in freesurfer 6.0 but we don't think it was correlated with this error.  I think we did set MCR_CACHE_ROOT to the user directory. We will try it again.   But where do we find this kvlSetMeshCollectionPostions.m file and how do we run it? I looked under $FREESURFER_HOME/bin and couldn't find it.

Our OS version is below:

$cat /etc/os-release

NAME="Ubuntu"

VERSION="18.04.4 LTS (Bionic Beaver)"

ID=ubuntu

ID_LIKE=debian

PRETTY_NAME="Ubuntu 18.04.4 LTS"

VERSION_ID="18.04"

We solved the  GLIBCXX_3.4.19 errors by unsetting LD_LIBRARY_PATH for the functions that this error occurred in (mri_robust_register, mri_convert, mri_mask, and mri_binarize).  

I am attaching the recon-all.log and hippocampal_subrields-T1.log

- Xiaoqian

============

Xiaoqian Chai, PhD

Assistant Professor

Canada Research Chair (Tier 2) in Developmental Cognitive Neuroscience 

Neurodevelopmental Disorders Group

Department of Neurology and Neurosurgery

McGill University

On Tue, Mar 24, 2020 at 12:08 AM Hoopes, Andrew <AHOOPES@mgh.harvard.edu> wrote:

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: 

 

 

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

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