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 http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting”

 

Best,

Michael