Not that I know of, but this is not a native FS script, it comes from the MNI, so it could be doing something we don't understand. Can you do an experiment for us? Can you run it outside of the container using reprozip (or something equivalent) to see all the files it touches?

On 10/5/18 5:31 AM, Jasper van den Bosch wrote:

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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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