Error running fmriprep 20.2.7: No such file or directory

[andreifoldes]

Description: When running the nipoppy command, an error occurs indicating that a required file is missing. Below are the details of the command and the error message.

Command:

nipoppy run --dataset-root /cubric/collab/487_mvpa/poppy-effex/dataset --pipeline fmriprep

Terminal Output:

2024-08-07 10:53:55,984 [    INFO] Loading config from /cubric/collab/487_mvpa/poppy-effex/dataset/global_config.json
WARNING  Pipeline version not specified, using version 20.2.7                                                                                                                   pipeline.py:326
2024-08-07 10:53:55,993 [ WARNING] Pipeline version not specified, using version 20.2.7
2024-08-07 10:53:55,996 [    INFO] Writing the log to /cubric/collab/487_mvpa/poppy-effex/dataset/scratch/logs/run/fmriprep-20.2.7/fmriprep-20.2.7-20240807_1053.log
2024-08-07 10:53:55,998 [    INFO] ========== BEGIN RUN WORKFLOW ==========
2024-08-07 10:53:55,999 [    INFO] PipelineRunner(dpath_root=/cubric/collab/487_mvpa/poppy-effex/dataset, pipeline_name=fmriprep, pipeline_version=20.2.7, pipeline_step=None, participant_id=None, session_id=None, simulate=False, fpath_layout=None, logger=<Logger run (INFO)>, dry_run=False)
WARNING  Creating directory /cubric/collab/487_mvpa/poppy-effex/dataset/derivatives/fmriprep/20.2.7/work/fmriprep-20.2.7                                                            base.py:234
2024-08-07 10:53:56,006 [ WARNING] Creating directory /cubric/collab/487_mvpa/poppy-effex/dataset/derivatives/fmriprep/20.2.7/work/fmriprep-20.2.7
2024-08-07 10:53:56,021 [    INFO] Running on participant 126BPCP021001, session 1
2024-08-07 10:53:56,023 [    INFO] Building BIDSLayout with 2 ignore patterns: [re.compile('^(?!/sub-(126BPCP021001))'), re.compile('.*?/ses-(?!1)')]
2024-08-07 10:53:56,732 [    INFO] Loading descriptor from /cubric/collab/487_mvpa/poppy-effex/dataset/proc/descriptors/fmriprep-None.json
ERROR    Error running fmriprep 20.2.7 on participant 126BPCP021001, session 1: [Errno 2] No such file or directory:                                                            pipeline.py:352
         '/cubric/collab/487_mvpa/poppy-effex/dataset/proc/descriptors/fmriprep-None.json'                                                                                                     
2024-08-07 10:53:56,733 [   ERROR] Error running fmriprep 20.2.7 on participant 126BPCP021001, session 1: [Errno 2] No such file or directory: '/cubric/collab/487_mvpa/poppy-effex/dataset/proc/descriptors/fmriprep-None.json'
2024-08-07 10:53:56,735 [    INFO] Removing /cubric/collab/487_mvpa/poppy-effex/dataset/proc/pybids/bids_db/fmriprep-20.2.7
2024-08-07 10:53:56,738 [    INFO] Removing /cubric/collab/487_mvpa/poppy-effex/dataset/derivatives/fmriprep/20.2.7/work/fmriprep-20.2.7
2024-08-07 10:53:56,742 [    INFO] ========== END RUN WORKFLOW ==========

Steps to Reproduce:

1. Run the command: nipoppy run --dataset-root /cubric/collab/487_mvpa/poppy-effex/dataset --pipeline fmriprep
2. Observe the error message indicating the missing file.

Expected Behavior: The pipeline should run without errors, and all necessary files should be found.

Actual Behavior: The pipeline fails with an error indicating that the file /cubric/collab/487_mvpa/poppy-effex/dataset/proc/descriptors/fmriprep-None.json is missing.

Additional Information:

• The pipeline version used is 20.2.7.
• The error occurs for participant 126BPCP021001 and session 1.

---

[andreifoldes]

running below command does solve it actually, but I thing the default should apply here, no?

nipoppy run --dataset-root /cubric/collab/487_mvpa/poppy-effex/dataset --pipeline fmriprep --pipeline-version 20.2.7

[michellewang]

• This is indeed a bug in Nipoppy, see https://github.com/nipoppy/nipoppy/issues/298
• There is a fix in the works but it hasn’t been merged yet: https://github.com/nipoppy/nipoppy/pull/300
• In the meantime (as you have discovered) if you explicitly specify the pipeline version it should work :)