Unable to process datasets from NFS mounted storage

[sebastientourbier]

Error

RuntimeError: Command:
5ttgen freesurfer -nocrop -sgm_amyg_hipp /tmp/derivatives/cmp/sub-001/ses-20170714/anat/sub-001_ses-20170714_desc-aparcaseg_dseg.nii.gz mrtrix_5tt.nii.gz
Standard output:

Standard error:
5ttgen: 
5ttgen: Note that this script makes use of commands / algorithms that have relevant articles for citation. Please consult the help page (-help option) for more information.
5ttgen: 
5ttgen: Generated temporary directory: /tmp/derivatives/nipype/sub-001/ses-20170714/diffusion_pipeline/preprocessing_stage/mrtrix_5tt/5ttgen-tmp-EQMGFD/
Command:  mrconvert /tmp/derivatives/cmp/sub-001/ses-20170714/anat/sub-001_ses-20170714_desc-aparcaseg_dseg.nii.gz /tmp/derivatives/nipype/sub-001/ses-20170714/diffusion_pipeline/preprocessing_stage/mrtrix_5tt/5ttgen-tmp-EQMGFD/input.mif
5ttgen: Changing to temporary directory (/tmp/derivatives/nipype/sub-001/ses-20170714/diffusion_pipeline/preprocessing_stage/mrtrix_5tt/5ttgen-tmp-EQMGFD/)
Command:  labelconvert input.mif /opt/freesurfer/FreeSurferColorLUT.txt /opt/mrtrix3/share/mrtrix3/_5ttgen/FreeSurfer2ACT_sgm_amyg_hipp.txt indices.mif
Command:  mrcalc indices.mif 1 -eq cgm.mif
Command:  mrcalc indices.mif 2 -eq sgm.mif
Command:  mrcalc indices.mif 3 -eq  wm.mif
Command:  mrcalc indices.mif 4 -eq csf.mif
Command:  mrcalc indices.mif 5 -eq path.mif
Command:  mrcat cgm.mif sgm.mif wm.mif csf.mif path.mif - -axis 3 | mrconvert - result.mif -datatype float32
Command:  5ttcheck result.mif
Command:  mrconvert result.mif /tmp/derivatives/nipype/sub-001/ses-20170714/diffusion_pipeline/preprocessing_stage/mrtrix_5tt/mrtrix_5tt.nii.gz
5ttgen: Changing back to original directory (/tmp/derivatives/nipype/sub-001/ses-20170714/diffusion_pipeline/preprocessing_stage/mrtrix_5tt)
5ttgen: Deleting temporary directory /tmp/derivatives/nipype/sub-001/ses-20170714/diffusion_pipeline/preprocessing_stage/mrtrix_5tt/5ttgen-tmp-EQMGFD/
Traceback (most recent call last):
  File "/opt/mrtrix3/bin/5ttgen", line 56, in <module>
    app.complete()
  File "/opt/mrtrix3/lib/mrtrix3/app.py", line 268, in complete
    shutil.rmtree(tempDir)
  File "/opt/conda/envs/py27cmp-core/lib/python2.7/shutil.py", line 270, in rmtree
    onerror(os.rmdir, path, sys.exc_info())
  File "/opt/conda/envs/py27cmp-core/lib/python2.7/shutil.py", line 268, in rmtree
    os.rmdir(path)
OSError: [Errno 39] Directory not empty: '/tmp/derivatives/nipype/sub-001/ses-20170714/diffusion_pipeline/preprocessing_stage/mrtrix_5tt/5ttgen-tmp-EQMGFD/'
Return code: 1

What causes the error
I have been successfully running this code on datasets stored locally. The error appeared when we switched to processing a dataset from a NFS mounted storage.
See similar error at https://mail.python.org/pipermail/python-list/2009-July/543694.html

Solution
Until now, we did not find a solution for processing with success the dataset stored on the NFS mounted drive.

Workaround
Make a local copy of the dataset to be processed