It’s only happening for one subject, right? nu_correct isn’t actually a freesurfer tool, it’s an mni tool. I would try to troubleshoot this by installing a newer version of minc for osx: http://packages.bic.mni.mcgill.ca/minc-toolkit/MacOSX/minc-toolkit-1.9.16-20...
Then, set the following BEFORE sourcing freesurfer and try rerunning the failed recon:
export MINC_BIN_DIR=/opt/minc/1.9.16/bin export MINC_LIB_DIR=/opt/minc/1.9.16/lib
best 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 4:14 PM To: FS Help freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all error
External Email - Use Caution Hi Andrew,
I am on a mac pro running Sierra 10.12.6
Best, 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
On Tue, Mar 19, 2019 at 2:40 PM Hoopes, Andrew <AHOOPES@mgh.harvard.edumailto:AHOOPES@mgh.harvard.edu> wrote: 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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Daniel Callow <ddcc2442@gmail.commailto:ddcc2442@gmail.com> Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, March 19, 2019 at 10:45 AM To: FS Help <freesurfer@nmr.mgh.harvard.edumailto: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
--------------------------------------------------------
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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer