External Email - Use Caution Hi 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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@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.har > vard.edu_fswiki_BugReporting&d=DwIF-g&c=iORugZls2LlYyCAZRB3XLg&r=LfvXl > A0kIui4WmLLCYdWlZdLsYFY_HKuPRMZoERJi_o&m=lOOasQKo-5smKR_WagoWBOFxCVZA3 > 8xYpWHKJOqIVGU&s=hZ8c1_TEb9oDCsFUiTaioaVn7pRCbIkq9BrlyHA-jps&e= > <https://urldefense.proofpoint.com/v2/url?u=http-3A__surfer.nmr.mgh.harvard.edu_fswiki_BugReporting&d=DwIF-g&c=iORugZls2LlYyCAZRB3XLg&r=LfvXlA0kIui4WmLLCYdWlZdLsYFY_HKuPRMZoERJi_o&m=lOOasQKo-5smKR_WagoWBOFxCVZA38xYpWHKJOqIVGU&s=hZ8c1_TEb9oDCsFUiTaioaVn7pRCbIkq9BrlyHA-jps&e= > >" > > Best, > > Michael > > > _______________________________________________ > 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.harvard.edu_mailman_listinfo_freesurfer&d=DwIF-g&c=iORugZls2LlYyCAZRB3XLg&r=LfvXlA0kIui4WmLLCYdWlZdLsYFY_HKuPRMZoERJi_o&m=lOOasQKo-5smKR_WagoWBOFxCVZA38xYpWHKJOqIVGU&s=RJ3pNp6iSv3KoImUDqKyKKlfJax1r3VtjF-gcSU_E60&e= _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
