Hello,
I’ve got an error from mne-bids-pipeline that there are too many json files in my bids dataset:
Aborting pipeline run. The full traceback is:
Traceback (most recent call last):
File "/home/ma09/.conda/envs/my_mne1.3/lib/python3.10/site-packages/mne_bids_pipeline/_run.py", line 55, in wrapper
out = memory.cache(func)(*args, **kwargs)
File "/home/ma09/.conda/envs/my_mne1.3/lib/python3.10/site-packages/mne_bids_pipeline/_run.py", line 148, in wrapper
in_files = kwargs["in_files"] = self.get_input_fnames(**these_kwargs)
File "/home/ma09/.conda/envs/my_mne1.3/lib/python3.10/site-packages/mne_bids_pipeline/steps/init/_02_find_empty_room.py", line 43, in get_input_fnames_find_empty_room
bids_path_in.copy()
File "/home/ma09/.conda/envs/my_mne1.3/lib/python3.10/site-packages/mne_bids/path.py", line 987, in find_matching_sidecar
return _find_matching_sidecar(
File "/home/ma09/.conda/envs/my_mne1.3/lib/python3.10/site-packages/mne_bids/path.py", line 1552, in _find_matching_sidecar
raise RuntimeError(msg)
RuntimeError: Expected to find a single .json file associated with sub-01_task-main_run-01, but found 11:
/imaging/davis/Projects/SpeechMisperceptionMEEG/MNE-BIDS_data/sub-01/meg/sub-01_coordsystem.json
/imaging/davis/Projects/SpeechMisperceptionMEEG/MNE-BIDS_data/sub-01/meg/sub-01_task-main_run-01_meg.json
/imaging/davis/Projects/SpeechMisperceptionMEEG/MNE-BIDS_data/sub-01/meg/sub-01_task-main_run-02_meg.json
/imaging/davis/Projects/SpeechMisperceptionMEEG/MNE-BIDS_data/sub-01/meg/sub-01_task-main_run-03_meg.json
/imaging/davis/Projects/SpeechMisperceptionMEEG/MNE-BIDS_data/sub-01/meg/sub-01_task-main_run-04_meg.json
/imaging/davis/Projects/SpeechMisperceptionMEEG/MNE-BIDS_data/sub-01/meg/sub-01_task-main_run-05_meg.json
/imaging/davis/Projects/SpeechMisperceptionMEEG/MNE-BIDS_data/sub-01/beh/sub-01_task-main_run-01_beh.json
/imaging/davis/Projects/SpeechMisperceptionMEEG/MNE-BIDS_data/sub-01/beh/sub-01_task-main_run-02_beh.json
/imaging/davis/Projects/SpeechMisperceptionMEEG/MNE-BIDS_data/sub-01/beh/sub-01_task-main_run-03_beh.json
/imaging/davis/Projects/SpeechMisperceptionMEEG/MNE-BIDS_data/sub-01/beh/sub-01_task-main_run-04_beh.json
/imaging/davis/Projects/SpeechMisperceptionMEEG/MNE-BIDS_data/sub-01/beh/sub-01_task-main_run-05_beh.json
The search_str was "/imaging/davis/Projects/SpeechMisperceptionMEEG/MNE-BIDS_data/sub-01/**/sub-01*.json"
This is a MEG dataset which I converted to BIDS format using mne-bids. The json files which appear to cause the trouble are sidecar files for the behavioural data I saved to the beh/ subfolder like so:
|MNE-BIDS_data/
|— README
|— dataset_description.json
|— participants.json
|— participants.tsv
|— sub-01/
|------ sub-01_scans.tsv
|------ beh/
|--------- sub-01_task-main_run-01_beh.json
|--------- sub-01_task-main_run-01_beh.tsv
|--------- sub-01_task-main_run-02_beh.json
|--------- sub-01_task-main_run-02_beh.tsv
|--------- sub-01_task-main_run-03_beh.json
|--------- sub-01_task-main_run-03_beh.tsv
|--------- sub-01_task-main_run-04_beh.json
|--------- sub-01_task-main_run-04_beh.tsv
|--------- sub-01_task-main_run-05_beh.json
|--------- sub-01_task-main_run-05_beh.tsv
|------ meg/
The _beh.tsv files contain a bunch of additional info about the trials (which I couldn’t fit in the meg events) plus responses and response times. The sidecar files describe the variables in the .tsv files as per the bids specification. I thought adding these json files should be ok, but I am not sure.
Am I doing something wrong at the bids conversion stage or could this be a bug in mne-bids-pipeline?
Many thanks,
Máté
System info:
Platform: Linux-3.10.0-1160.el7.x86_64-x86_64-with-glibc2.17
Python: 3.10.9 | packaged by conda-forge | (main, Feb 2 2023, 20:20:04) [GCC 11.3.0]
Executable: /home/ma09/.conda/envs/my_mne1.3/bin/python
CPU: x86_64: 32 cores
Memory: 251.4 GB
mne: 1.3.0
numpy: 1.23.5 {OpenBLAS 0.3.21 with 32 threads}
scipy: 1.10.0
matplotlib: 3.6.3 {backend=module://matplotlib_inline.backend_inline}
sklearn: 1.2.1
numba: 0.56.4
nibabel: 5.0.1
nilearn: 0.10.0
dipy: 1.6.0
openmeeg: 2.5.5
cupy: Not found
pandas: 1.5.3
pyvista: 0.38.2 {OpenGL could not be initialized}
pyvistaqt: 0.9.1
ipyvtklink: 0.2.2
vtk: 9.2.5
qtpy: 2.3.0 {None=None}
ipympl: Not found
pyqtgraph: 0.13.1
pooch: v1.6.0
mne_bids: 0.12
mne_nirs: Not found
mne_features: Not found
mne_qt_browser: 0.4.0
mne_connectivity: Not found
mne_icalabel: Not found
