External Email - Use Caution
Hi Doug,
Ok I'll verify the creation of the symlink today. Thank you for following-up.
Could you also maybe give me some details about what this termination status means? : nu_correct: crashed while running nu_estimate_np_and_em (termination status=256)
Perhaps I can try to debug if I knew a little more. Sorry if this information is easily available. I couldn't find what the termination status means.
Best, Michael
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Greve, Douglas N.,Ph.D. Sent: Thursday, September 19, 2019 7:41 AM To: freesurfer@nmr.mgh.harvard.edu; Dicamillo, Robert RDICAMILLO@mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all on a cluster error
Not sure then. I've seen cases where the creation of symbolic links was not possible on a cluster. It does not look like this is the problem, but it could be doing something behind the scenes. Can you verify that you can create a symlink from a program on the cluster? I've cc'ed Rob D who can help debug this problem if it persists. doug
On 9/17/19 1:57 PM, Lauricella, Michael wrote:
External Email - Use CautionHi Douglas,
Yes it does fine. On the cluster, this same error happens for all subjects.
Thank you for your help!
Best, Michael
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Greve, Douglas N.,Ph.D. Sent: Tuesday, September 17, 2019 10:50 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all on a cluster error
Does it run properly off the cluster for this data set?
On 9/17/19 1:45 PM, Lauricella, Michael wrote:
External Email - Use Caution
Dear Freesurfer Experts,
I have a an error when running recon-all on a computing cluster. I've checked the environment and so have some of my more knowledgeable colleagues but we can't see anything wrong with the environment. I was wondering if anyone else has experienced difficulties like the one below when trying to run recon-all on a computing cluster and might have some advice. Error of my run is below and the full log file is attached. Thank you in advance for your help!
"Iteration 1 Wed Aug 7 13:53:08 PDT 2019
nu_correct -clobber ./tmp.mri_nu_correct.mni.18980/nu0.mnc ./tmp.mri_nu_correct.mni.18980/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.18980/0/ -iterations 1000 -distance 50
[mlauricella@qb3-id115:/mnt/freesurfer_subjs/SUBJECT_ID/mri/] [2019-08-07 13:53:08] running:
/mnt/neuroimaging/FreeSurfer/V6.0.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.18980/0/ ./tmp.mri_nu_correct.mni.18980/nu0.mnc ./tmp.mri_nu_correct.mni.18980/nu1.imp
Assertion failed at line 742 in file templates/CachedArray.cc
nu_estimate_np_and_em: crashed while running volume_stats (termination status=256)
nu_correct: crashed while running nu_estimate_np_and_em (termination status=256)
ERROR: nu_correct
Linux qb3-id115 3.10.0-957.21.3.el7.x86_64 #1 SMP Tue Jun 18 16:35:19 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s SUBJECT_ID exited with ERRORS at Wed Aug 7 13:53:09 PDT 2019
To report a problem, see https://urldefense.proofpoint.com/v2/url?u=http-3A__surfer.nmr.mgh.ha r vard.edu_fswiki_BugReporting&d=DwIF-g&c=iORugZls2LlYyCAZRB3XLg&r=LfvX l A0kIui4WmLLCYdWlZdLsYFY_HKuPRMZoERJi_o&m=lOOasQKo-5smKR_WagoWBOFxCVZA 3 8xYpWHKJOqIVGU&s=hZ8c1_TEb9oDCsFUiTaioaVn7pRCbIkq9BrlyHA-jps&e= <https://urldefense.proofpoint.com/v2/url?u=http-3A__surfer.nmr.mgh.harvard.e... >"
Best,
Michael
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.har v ard.edu_mailman_listinfo_freesurfer&d=DwIF-g&c=iORugZls2LlYyCAZRB3XLg & r=LfvXlA0kIui4WmLLCYdWlZdLsYFY_HKuPRMZoERJi_o&m=lOOasQKo-5smKR_WagoWB O FxCVZA38xYpWHKJOqIVGU&s=RJ3pNp6iSv3KoImUDqKyKKlfJax1r3VtjF-gcSU_E60&e =
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harv ard.edu_mailman_listinfo_freesurfer&d=DwIF-g&c=iORugZls2LlYyCAZRB3XLg& r=LfvXlA0kIui4WmLLCYdWlZdLsYFY_HKuPRMZoERJi_o&m=lOOasQKo-5smKR_WagoWBO FxCVZA38xYpWHKJOqIVGU&s=RJ3pNp6iSv3KoImUDqKyKKlfJax1r3VtjF-gcSU_E60&e=
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harv ard.edu_mailman_listinfo_freesurfer&d=DwIGaQ&c=iORugZls2LlYyCAZRB3XLg& r=LfvXlA0kIui4WmLLCYdWlZdLsYFY_HKuPRMZoERJi_o&m=keqUrwoinWgFRftQn5LJ4C 0wzRMsCQ0crSLg1xpdBmg&s=0i7zbP6Xv12mxJNAUKma-MVXBnB118LLcjOUsN_lct8&e=
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...