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
>>> =
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>>
>>
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>> 0wzRMsCQ0crSLg1xpdBmg&s=0i7zbP6Xv12mxJNAUKma-MVXBnB118LLcjOUsN_lct8&e=
>
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