Could not start qsiprep 1.1.1, `ValueError: Protocol not known: 'bids'`

[arovai]

Summary

Could not start qsiprep, error mentions ValueError: Protocol not known: 'bids'.

Additional details

• QSIPrep version: 1.1.1
• Docker version: 29.2.1
• Singularity version: n/a

What were you trying to do?

Launching qsiprep on a BIDS dataset (passed bids/validator:2.4.0).

What did you expect to happen?

Should launch qsiprep and exit gracefully.

What actually happened?

Crashed immediately

Reproducing the bug

To be run on sample data (~/rawdata is a BIDS dataset)

sudo docker run -ti --rm -v ~/rawdata:/data -v ~/derivatives:/derivatives -v /opt/freesurfer/.license:/opt/freesurfer/license.txt pennlinc/qsiprep:1.1.1 /data /derivatives/qsiprep_1.1.1 participant --fs-license-file /opt/freesurfer/license.txt --output-resolution 1.5

Complete output

Traceback (most recent call last):
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/upath/_protocol.py", line 50, in _fsspec_protocol_equals
    o0 = _fsspec_registry_map[p0]
  File "/opt/conda/envs/qsiprep/lib/python3.10/collections/__init__.py", line 986, in __getitem__
    return self.__missing__(key)            # support subclasses that define __missing__
  File "/opt/conda/envs/qsiprep/lib/python3.10/collections/__init__.py", line 978, in __missing__
    raise KeyError(key)
KeyError: 'bids'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/opt/conda/envs/qsiprep/bin/qsiprep", line 7, in <module>
    sys.exit(main())
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep/cli/run.py", line 42, in main
    parse_args()
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep/cli/parser.py", line 762, in parse_args
    config.from_dict({})
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep/config.py", line 721, in from_dict
    execution.load(settings, init=initialize('execution'), ignore=ignore)
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep/config.py", line 251, in load
    cls.init()
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep/config.py", line 496, in init
    cls._layout = BIDSLayout(
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/bids/layout/layout.py", line 177, in __init__
    _indexer(self)
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/bids/layout/index.py", line 155, in __call__
    self._index_metadata()
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/bids/layout/index.py", line 464, in _index_metadata
    target = self._layout._root.joinpath(
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/upath/implementations/local.py", line 272, in joinpath
    if not compatible_protocol("", *other):
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/upath/_protocol.py", line 127, in compatible_protocol
    if other_protocol and not _fsspec_protocol_equals(other_protocol, protocol):
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/upath/_protocol.py", line 52, in _fsspec_protocol_equals
    raise ValueError(f"Protocol not known: {p0!r}")
ValueError: Protocol not known: 'bids'

[pollaro]

Can we get an update on this? I've had the same error

[mattcieslak]

Are you both using BIDS URI's for your fieldmaps?

[arovai]

I use BIDS URI to link the dwi with AP to the other with PA (BIDS URI in IdendedFor in sidecar).

[pollaro]

Yes, I am using BIDS URI. Shoot, did I miss that we weren't supposed to? I get my pipelines between projects mixed up...

[tsalo]

Unfortunately, QSIPrep doesn't support BIDS-URIs yet. We plan to at some point, but haven't figured it out yet (see #658). It looks like @karl-koschutnig did write a script that will downgrade BIDS-URIs in a dataset's IntendedFors to relative paths that should work in QSIPrep (#658 (comment)).