Docker documentation

[mckenziephagen]

What would you like changed/added and why?

With the update of MRIQC enabled to incorporate datalad and be able to pull data down from OpenNeuro using datalad, the Docker instructions with the :ro (readonly) tag for the BIDS directory volume fail. I don't have the exact error message currently (macOS update woes), but it was something along the lines of trying to download on a read only filesystem.

I can update the documentation, as long as there's no potential problems with dropping the :ro in the volume binding for the BIDS directory.

Do you have any interest in helping improve the documentation?

Yes

Do you have any suggestions for the new documents?

@oesteban tagging for your thoughts.
No response

[mckenziephagen]

Full output/error.

(new_dl) kenziepaige@MacBook-Pro-209 MRIQC % docker run -it --rm -v $bids_dir:/data:ro -v $output_dir:/out nipreps/mriqc:latest /data /out participant --participant_label 0010
WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested
------------------------------------------------------------------
  Running MRIQC version 24.1.0.dev0+gd5b13cb5.d20240826
  ----------------------------------------------------------------

  NOTICE
  Copyright © The NiPreps Developers.
  
  This product includes software developed by
  the NiPreps Community (https://nipreps.org/).
  
  Portions of this software were developed at the Department of
  Psychology at Stanford University, Stanford, CA, US.
  
  This software contains code ultimately derived from the
  PCP Quality Assessment Protocol (QAP;
  http://preprocessed-connectomes-project.org/quality-assessment-protocol)
  by C. Craddock, S. Giavasis, D. Clark, Z. Shezhad, and J. Pellman.
  
  This software is also distributed as a Docker container image.
  The bootstrapping file for the image ("Dockerfile") is licensed
  under the MIT License.

  ----------------------------------------------------------------

  * BIDS dataset path: /data.
  * Output folder: /out.
  * Analysis levels: ['participant'].
------------------------------------------------------------------

2024-12-05 00:29:21 | IMPORTANT | mriqc            | DataLad dataset identified, attempting to `datalad get` unavailable files.
get(error): sub-0010/func/sub-0010_task-gstroop_acq-seq_bold.nii.gz (file) [git-annex: .git/annex/tmp: createDirectory: permission denied (Read-only file system)]
get(error): sub-0010/func/sub-0010_task-anticipation_acq-seq_bold.nii.gz (file) [git-annex: .git/annex/tmp: createDirectory: permission denied (Read-only file system)]
get(error): sub-0010/func/sub-0010_task-restingstate_acq-mb3_bold.nii.gz (file) [git-annex: .git/annex/tmp: createDirectory: permission denied (Read-only file system)]
get(error): sub-0010/func/sub-0010_task-faces_acq-mb3_bold.nii.gz (file) [git-annex: .git/annex/tmp: createDirectory: permission denied (Read-only file system)]
get(error): sub-0010/dwi/sub-0010_dwi.nii.gz (file) [git-annex: .git/annex/tmp: createDirectory: permission denied (Read-only file system)]
get(error): sub-0010/anat/sub-0010_T1w.nii.gz (file) [git-annex: .git/annex/tmp: createDirectory: permission denied (Read-only file system)]
get(error): sub-0010/func/sub-0010_task-emomatching_acq-seq_bold.nii.gz (file) [git-annex: .git/annex/tmp: createDirectory: permission denied (Read-only file system)]
get(error): sub-0010/func/sub-0010_task-workingmemory_acq-seq_bold.nii.gz (file) [git-annex: .git/annex/tmp: createDirectory: permission denied (Read-only file system)]
action summary:
  get (error: 8)
Traceback (most recent call last):
  File "/opt/conda/bin/mriqc", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/opt/conda/lib/python3.11/site-packages/mriqc/cli/run.py", line 43, in main
    parse_args(argv)
  File "/opt/conda/lib/python3.11/site-packages/mriqc/cli/parser.py", line 658, in parse_args
    initialize_meta_and_data()
  File "/opt/conda/lib/python3.11/site-packages/mriqc/utils/misc.py", line 447, in initialize_meta_and_data
    _datalad_get(dataset)
  File "/opt/conda/lib/python3.11/site-packages/mriqc/utils/misc.py", line 282, in _datalad_get
    return get(
           ^^^^
  File "/opt/conda/lib/python3.11/site-packages/datalad/interface/base.py", line 773, in eval_func
    return return_func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/lib/python3.11/site-packages/datalad/interface/base.py", line 763, in return_func
    results = list(results)
              ^^^^^^^^^^^^^
  File "/opt/conda/lib/python3.11/site-packages/datalad_next/patches/interface_utils.py", line 287, in _execute_command_
    raise IncompleteResultsError(
datalad.support.exceptions.IncompleteResultsError: Command did not complete successfully. 8 failed:
[{'action': 'get',
  'annexkey': 'MD5E-s76037251--344f061a3165c71e36b98ad1649c3c8c.nii.gz',
  'error_message': 'git-annex: .git/annex/tmp: createDirectory: permission '
                   'denied (Read-only file system)',
  'path': '/data/sub-0010/func/sub-0010_task-gstroop_acq-seq_bold.nii.gz',
  'refds': '/data',
  'status': 'error',
  'type': 'file'},
 {'action': 'get',
  'annexkey': 'MD5E-s62372280--f49e3ef7ef162eac055c6e683720584b.nii.gz',
  'error_message': 'git-annex: .git/annex/tmp: createDirectory: permission '
                   'denied (Read-only file system)',
  'path': '/data/sub-0010/func/sub-0010_task-anticipation_acq-seq_bold.nii.gz',
  'refds': '/data',
  'status': 'error',
  'type': 'file'},
 {'action': 'get',
  'annexkey': 'MD5E-s147699014--93fa2960425581fa03a1f5fcad7cf2c6.nii.gz',
  'error_message': 'git-annex: .git/annex/tmp: createDirectory: permission '
                   'denied (Read-only file system)',
  'path': '/data/sub-0010/func/sub-0010_task-restingstate_acq-mb3_bold.nii.gz',
  'refds': '/data',
  'status': 'error',
  'type': 'file'},
 {'action': 'get',
  'annexkey': 'MD5E-s266328294--5cfe464f08b38cfcb20d4d9977db7057.nii.gz',
  'error_message': 'git-annex: .git/annex/tmp: createDirectory: permission '
                   'denied (Read-only file system)',
  'path': '/data/sub-0010/func/sub-0010_task-faces_acq-mb3_bold.nii.gz',
  'refds': '/data',
  'status': 'error',
  'type': 'file'},
 {'action': 'get',
  'annexkey': 'MD5E-s13773098--1a0ea41fbc2a9d6f3637fd9a4dfced0c.nii.gz',
  'error_message': 'git-annex: .git/annex/tmp: createDirectory: permission '
                   'denied (Read-only file system)',
  'path': '/data/sub-0010/dwi/sub-0010_dwi.nii.gz',
  'refds': '/data',
  'status': 'error',
  'type': 'file'},
 {'action': 'get',
  'annexkey': 'MD5E-s5889514--b3711e82a17c752c68588fefb72b36fe.nii.gz',
  'error_message': 'git-annex: .git/annex/tmp: createDirectory: permission '
                   'denied (Read-only file system)',
  'path': '/data/sub-0010/anat/sub-0010_T1w.nii.gz',
  'refds': '/data',
  'status': 'error',
  'type': 'file'},
 {'action': 'get',
  'annexkey': 'MD5E-s41518453--988ea169d4f0440b8395f45f1e7b59a0.nii.gz',
  'error_message': 'git-annex: .git/annex/tmp: createDirectory: permission '
                   'denied (Read-only file system)',
  'path': '/data/sub-0010/func/sub-0010_task-emomatching_acq-seq_bold.nii.gz',
  'refds': '/data',
  'status': 'error',
  'type': 'file'},
 {'action': 'get',
  'annexkey': 'MD5E-s50284854--53b20ac38249161182afb5f96a99ade3.nii.gz',
  'error_message': 'git-annex: .git/annex/tmp: createDirectory: permission '
                   'denied (Read-only file system)',
  'path': '/data/sub-0010/func/sub-0010_task-workingmemory_acq-seq_bold.nii.gz',
  'refds': '/data',
  'status': 'error',
  'type': 'file'}]

Leaving off the :ro runs without problems.

[oesteban]

Thanks! Yes, we do need to update the documentation. I think the right way to do this is: (i) keep the recommendation of :ro, but (ii) extend it to say that, if you plan to use datalad and have MRIQC datalad-get data, then of course you need to download the data somewhere and that somewhere cannot be protected with :ro.

Another thing that you are not reporting here and IS NOT in the docs, is that you want to run docker with a given user (and potentially group). That can be done with -u and -g.

The nipreps' docs are here https://www.nipreps.org/apps/docker/, probably worth updating there and reducing anything there is in MRIQC's docs to a link to this page.

[oesteban]

Closing as this has been addressed with #1367 and nipreps/nipreps.github.io#47.