I don't really know myself. This part runs a program from a 3rd party -- the MNI (n3 bias field correction); we did not write it so it is hard for us to debug. We often have problems with this program, so unfortunately, it does not surprise me
On 9/19/19 12:42 PM, Lauricella, Michael wrote: > 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
