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
>>
>>
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>> =
>
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