External Email - Use Caution
Yes, everything was run on the same machine with identical settings.
On Tue, Mar 24, 2020 at 12:49 PM Iglesias Gonzalez, Juan E. < JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:
Thanks Xiaoqian,
When it worked, was it on the same machine?
Also: MCR_CACHE_ROOT will be set to a random directory by the software to avoid collisions…
Cheers,
/E
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Xiaoqian Chai xiaoqian.chai@gmail.com *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Tuesday, March 24, 2020 at 12:24 *To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] Error in segmentation of the hippocampal subfields: /tmp/MCR_3634872073/.mcrCache8.4 error
External Email - Use Caution *I forgot to say that running segmentHA_T1.sh the second or the third time was successful for some subjects with the /tmp/MCR.... error.
On Tue, Mar 24, 2020 at 11:56 AM Xiaoqian Chai xiaoqian.chai@gmail.com wrote:
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:
- The recon and hippocampal log files.
- 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)
*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:
[image: 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
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