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