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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@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 <rdicami...@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 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.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.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.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.edu_mailman_listinfo_freesurfer&d=DwIGaQ&c=iORugZls2LlYyCAZRB3XLg&r=LfvXlA0kIui4WmLLCYdWlZdLsYFY_HKuPRMZoERJi_o&m=keqUrwoinWgFRftQn5LJ4C0wzRMsCQ0crSLg1xpdBmg&s=0i7zbP6Xv12mxJNAUKma-MVXBnB118LLcjOUsN_lct8&e= _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
