File Permissions issues for MCRIBS outputs

[scott-huberty]

Running the latest version of Nibabies (24) using Singularity on an HPC.

For some reason, a lot of the files being written to out/sourcedata/mcribs Grant no permissions. This causes Nibabies to crash when the pipeline tries to access those files downstream in the pipeline. Here is just one example

command

singularity run -e \
  -B /home/path/to/bids:/data:ro \
  -B /home/path/to/derivatives/Nibabies:/out \
  -B /home/path/to/scratch:/scratch \
  -B /home/path/to/freesurfer/license.txt:/opt/freesurfer/license.txt:ro \
  -B /home/path/to/derivatives/precomputed:/opt/derivatives/precomputed \
  /home/path/to/nibabies_latest.sif \
  /data /out participant \
  --age-months 1 \
  --participant-label 999 \
  --derivatives /opt/derivatives/precomputed \
  -w /scratch \
  --surface-recon-method mcribs \
  --cifti-output 91k \
  --verbose

Traceback (most recent call last):
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
    result = self._run_interface(execute=True)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
    return self._run_command(execute)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command
    raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node mcribs_recon.

Cmdline:
	MCRIBReconAll --deformablefastcollision --deformablejointhresh 1.000000 -nthreads 8 --surfrecon --surfreconmethod Deformable sub-1462_ses-newborn
Stdout:
	sub-1462_ses-newborn 1.0 True False False

	Reconstructing cortical surfaces of sub-1462_ses-newborn session 0
	No input T1-weighted image found, using only T2-weighted image
	> /opt/MCRIBS/MIRTK/MIRTK-install/lib/tools/calculate-element-wise /out/sourcedata/mcribs/sub-1462_ses-newborn/TissueSeg/sub-1462_ses-newborn_all_labels_manedit.nii.gz -mask 0 -set 1 -pad 0 -out /out/sourcedata/mcribs/sub-1462_ses-newborn/TissueSeg/sub-1462_ses-newborn_brain_mask.nii.gz binary

	IOError: Cifstream::Open: Failed to open file /out/sourcedata/mcribs/sub-1462_ses-newborn/TissueSeg/sub-1462_ses-newborn_all_labels_manedit.nii.gz

upon further inspection of this file, you see what I mean:

ls -l /home/path/to/derivatives/Nibabies/sourcedata/mcribs/sub-1462_ses-newborn/TissueSeg/

total 452
lrwxrwxrwx 1 hubers2 l3_humphreys_lab     38 Sep  5 16:52 sub-1462_ses-newborn_all_labels_manedit.nii.gz -> sub-1462_ses-newborn_all_labels.nii.gz
---------- 1 hubers2 l3_humphreys_lab 256056 Sep  5 16:52 sub-1462_ses-newborn_all_labels.nii.gz
lrwxrwxrwx 1 hubers2 l3_humphreys_lab     36 Sep  5 16:52 sub-1462_ses-newborn_t2w_restore.nii.gz -> ../RawT2/sub-1462_ses-newborn.nii.gz

Right now the work around seems to be changing the permissions for these files and running the pipeline again (leaving the work and out directories intact so Nibabies hopefully picks up where it left off). 🤞

e.g.

chmod -R a+r  /home/hubers2/MRI_Processing/BABIES/MRI/newborn/derivatives/Nibabies/sourcedata/mcribs/sub-1462_ses-newborn/

Not sure if this is something that can/should be fixed by specifying the permissions when writing the files. If so, I really hope that the fix can be made in the Python stack (e.g. in Nibabies or Nipype).