External Email - Use Caution We are trying to run recon_all inside an fmriprep singularity container, but are running into an issue with nu_correct. It says it cannot write to disk, however there is plenty of space on the tmpdir and output dir. Does this script try to write to any other locations? Because this would fail inside the container, where each writable location has to be 'mounted'.
Error message: ncendef: ncid 5: No space left on device Error outputting volume: possibly disk full? nu_evaluate: crashed while running evaluate_field (termination status=139) nu_correct: crashed while running nu_evaluate (termination status=65280) ERROR: nu_correct Command ran: nu_correct -clobber ./tmp.mri_nu_correct.mni.1121/nu0.mnc ./tmp.mri_nu_correct.mni.1121/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1121/0/ -iterations 1000 -distance 50 [xxx@yyyy.cluster:/data/BIDS/derivatives/freesurfer/sub-1/mri/] [2018-10-04 14:59:29] running: /opt/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.1121/0/ ./tmp.mri_nu_correct.mni.1121/nu0.mnc ./tmp.mri_nu_correct.mni.1121/nu1.imp this issue at the fmriprep repo: https://github.com/poldracklab/fmriprep/issues/1308 possibly related: https://github.com/freesurfer/freesurfer/issues/462 Many thanks for any advice, Jasper van den Bosch
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