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

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:

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:

[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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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)

http://www.jeiglesias.com

*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:

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:

[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

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Hi Xiaoqian,

Sorry, I didn’t realize until now that MCR_CACHE_ROOT was actually being overwritten in the segmenHA setup script, so setting the env var beforehand actually did nothing :/. Since this error is somewhat sporadic, I still think it’s worth tracking down whether saving to a different tmp dir will fix things. Google seems to lead me in that direction, and I’m not really sure how else to troubleshoot this. In the future, we will make an easier way to overwrite MCR_CACHE_ROOT on the cmdline, but for now you might need some manual intervention. In the script $FREESURFER_HOME/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh, try changing the line:

MCR_CACHE_ROOT=$( echo "/tmp/MCR_${RANDOMNUMBER}/" | tr -d ' ' ) ;

To:

MCR_CACHE_ROOT=$( echo "/${HOME}/MCR_${RANDOMNUMBER}/" | tr -d ' ' ) ;

This will force your home dir as the cache directory. Not sure if this will fix things, but let’s hope!

Best Andrew

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Xiaoqian Chai xiaoqian.chai@gmail.com Reply-To: FS Help freesurfer@nmr.mgh.harvard.edu Date: Tuesday, March 24, 2020 at 1:58 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

External Email - Use Caution Somehow, setting MCR_CACHE_ROOT to the user directory only solves the problem sometimes. Other times, it still looks for things in the /tmp directory.

I checked with our admin regarding /tmp deletion, only things that are more than three days old get deleted but segmentHA_T1 only take about 30 minutes to run.

On Tue, Mar 24, 2020 at 12:52 PM Xiaoqian Chai <xiaoqian.chai@gmail.commailto:xiaoqian.chai@gmail.com> wrote: 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.edumailto: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) http://www.jeiglesias.com

From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Xiaoqian Chai <xiaoqian.chai@gmail.commailto:xiaoqian.chai@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, March 24, 2020 at 12:24 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.commailto: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.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ@mgh.harvard.edumailto:JIGLESIASGONZALEZ@mgh.harvard.edu> Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, March 23, 2020 at 5:56 PM To: FS Help <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Pascale Patenaude <pascalepatenaude@hotmail.commailto:pascalepatenaude@hotmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, March 23, 2020 at 16:55 To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto: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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer