fatal: detected dubious ownership in repository at '/opt/MCRIBS'

[scott-huberty]

Busy day.. Sorry in advance but I'm going to start initiating threads here as I run into issues that I think might warrant a fix/improvement. If that is confirmed by the team, then I'll escalate it to a ticket. If not then I think at least it can still be helpful to someone in the future, assuming I'm not the only one that will run into these issues!

First up in a slew of permissions errors I've been running into today. Running The latest Nibabies via singularity on an HPC:

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

I got this fatal: detected dubious ownership in repository at '/opt/MCRIBS' error which prevents any MCRIBS commands from being run:

Full Stack trace

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
	Traceback (most recent call last):
	  File "/opt/MCRIBS/bin/../MIRTK/MIRTK-install/lib/tools/recon-neonatal-cortex", line 932, in <module>
	    recon_neonatal_cortex(config=config, section=args.section, config_vars=config_vars,
	  File "/opt/MCRIBS/bin/../MIRTK/MIRTK-install/lib/tools/recon-neonatal-cortex", line 564, in recon_neonatal_cortex
	    require_regions_mask(config, section, config_vars, stack, verbose)
	  File "/opt/MCRIBS/bin/../MIRTK/MIRTK-install/lib/tools/recon-neonatal-cortex", line 185, in require_regions_mask
	    require_input_brain_mask(config, section, config_vars, stack)
	  File "/opt/MCRIBS/bin/../MIRTK/MIRTK-install/lib/tools/recon-neonatal-cortex", line 165, in require_input_brain_mask
	    neoctx.binarize(
	  File "/opt/MCRIBS/MIRTK/MIRTK-install/lib/python/mirtk/deformable/neonatal_cortex.py", line 759, in binarize
	    run('calculate-element-wise', args=[segmentation], opts=opts)
	  File "/opt/MCRIBS/MIRTK/MIRTK-install/lib/python/mirtk/deformable/neonatal_cortex.py", line 183, in run
	    _run(tool, args=args, opts=opts, showcmd=showcmd, threads=threads)
	  File "/opt/MCRIBS/MIRTK/MIRTK-install/lib/python/mirtk/subprocess.py", line 296, in run
	    raise e
	  File "/opt/MCRIBS/MIRTK/MIRTK-install/lib/python/mirtk/subprocess.py", line 281, in run
	    check_call(argv, verbose=1 if showcmd else 0)
	  File "/opt/MCRIBS/MIRTK/MIRTK-install/lib/python/mirtk/subprocess.py", line 157, in check_call
	    _call(argv, verbose=verbose, execfunc=subprocess.check_call)
	  File "/opt/MCRIBS/MIRTK/MIRTK-install/lib/python/mirtk/subprocess.py", line 145, in _call
	    return execfunc(argv)
	           ^^^^^^^^^^^^^^
	  File "/opt/conda/envs/nibabies/lib/python3.11/subprocess.py", line 413, in check_call
	    raise CalledProcessError(retcode, cmd)
	subprocess.CalledProcessError: Command '['/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']' returned non-zero exit status 5.

	Running command:
		MCRIBSurfReconDeformable sub-1462_ses-newborn 1.0 True False False
Stderr:
	fatal: detected dubious ownership in repository at '/opt/MCRIBS'
	To add an exception for this directory, call:

		git config --global --add safe.directory /opt/MCRIBS

For me the work around was entering the container and adding the suggested exception for the MCRIBS repository i.e.

singularity shell --cleanenv /home/path/to/nibabies_latest.sif

git config --global --add safe.directory /opt/MCRIBS

And FWIW I initially thought it might be a permissions issue, but the permissions of the directory look fine

ls -l /opt

drwxr-xr-x  8 root root 222 Jul 11 13:55 MCRIBS

crash-20240905-165240-hubers2-mcribs_recon-d77c9839-6a40-4e83-a1db-ce6d84aef7fe.txt

[mgxd]

IIRC, the message

fatal: detected dubious ownership in repository at '/opt/MCRIBS'
	To add an exception for this directory, call:

		git config --global --add safe.directory /opt/MCRIBS

is just a warning that gets printed to the log, not the actual reason for the crash - probably since we are git cloning in the MCRIBS container and then copying it over for the nibabies one. I think it can be resolved by adding that command (git config --global --add safe.directory /opt/MCRIBS) directly into the Dockerfile.

In your case, looks like there was a problem with loading the segmentations.

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

[scott-huberty]

In your case, looks like there was a problem with loading the segmentations.

Ah I thought that these were two separate issues and that this dubious ownership error was initially causing the crash. And see my other ticket for this IO error.