Hi Daniel, I’ve never seen this error before. I assume you’re on a mac – what version are you using? Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Daniel Callow ddcc2442@gmail.com Reply-To: FS Help freesurfer@nmr.mgh.harvard.edu Date: Tuesday, March 19, 2019 at 10:45 AM To: FS Help freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] recon-all error
External Email - Use Caution Hello, I am trying to run recon-all on a dataset and am running into errors with one of my subjects.
I get an error at the following point
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Iteration 1 Tue Mar 19 10:11:08 EDT 2019
nu_correct -clobber ./tmp.mri_nu_correct.mni.40972/nu0.mnc ./tmp.mri_nu_correct.mni.40972/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.40972/0/ -iterations 1000 -distance 50
[administrator@hlhp-105.umd.edu:/Volumes/DANIEL/freesurfer/Ex.AES118/mri/] [2019-03-19 10:11:09] running:
/Applications/freesurfer//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.40972/0/ ./tmp.mri_nu_correct.mni.40972/nu0.mnc ./tmp.mri_nu_correct.mni.40972/nu1.imp
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
ncvarget: ncid 4; varid 6: Argument list too long
miicv_get: MINC package entry point
nu_estimate_np_and_em: crashed while running mincmath (termination status=768)
nu_correct: crashed while running nu_estimate_np_and_em (termination status=768)
ERROR: nu_correct
Darwin hlhp-105.umd.eduhttp://hlhp-105.umd.edu 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct 10 20:06:00 PDT 2018; root:xnu-3789.73.24~1/RELEASE_X86_64 x86_64
recon-all -s Ex.AES118 exited with ERRORS at Tue Mar 19 10:11:18 EDT 2019
For more details, see the log file /Volumes/DANIEL/freesurfer/Ex.AES118/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Any help you can provide for troubleshooting would be greatly appreciated. Daniel Callow PhD Student, Neuroscience and Cognitive Science Exercise for Brain Health Lab University of Maryland, College Park ddcc2442@gmail.commailto:ddcc2442@gmail.com 443-254-6298