Hi,
I am getting the below error whenever I set a run number different than ‘01’ in the maxwell filter reference run parameter (mf_reference_run) in mne-bids-pipeline.
[16:19:22] │ ⏳️ preprocessing/_01_data_quality sub-02 run-02 Finding flat channels and noisy channels using Maxwell filtering.
Opening raw data file /imaging/davis/Projects/SpeechMisperceptionMEEG/MNE-BIDS_data/sub-02/meg/sub-02_task-main_run-02_meg.fif...
joblib.externals.loky.process_executor._RemoteTraceback:
"""
Traceback (most recent call last):
File "/home/ma09/.conda/envs/my_mne1.4/lib/python3.11/site-packages/mne_bids_pipeline/_run.py", line 54, in wrapper
out = memory.cache(func)(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ma09/.conda/envs/my_mne1.4/lib/python3.11/site-packages/mne_bids_pipeline/_run.py", line 147, in wrapper
in_files = kwargs["in_files"] = self.get_input_fnames(**these_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ma09/.conda/envs/my_mne1.4/lib/python3.11/site-packages/mne_bids_pipeline/steps/preprocessing/_01_data_quality.py", line 46, in get_input_fnames_data_quality
in_files = _get_raw_paths(
^^^^^^^^^^^^^^^
File "/home/ma09/.conda/envs/my_mne1.4/lib/python3.11/site-packages/mne_bids_pipeline/_import_data.py", line 564, in _get_raw_paths
raw_fname = _read_json(_empty_room_match_path(bids_path_in, cfg))[
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ma09/.conda/envs/my_mne1.4/lib/python3.11/site-packages/mne_bids_pipeline/_io.py", line 17, in _read_json
with open(fname, "r", encoding="utf-8") as f:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: '/imaging/davis/Projects/SpeechMisperceptionMEEG/data/derivatives/mne-bids-pipeline/sub-01/meg/sub-01_task-main_run-01_emptyroommatch.json'
So the pipeline is looking for a file named ‘sub-01_task-main_run-01_emptyroommatch.json’, whereas the actual file is called sub-01_task-main_run-03_emptyroommatch.json as I set mf_reference_run = '03' as it is recommended that a middle run should be used in this situation.
Does this seem like a bug or am I doing something wrong?
Many thanks,
Máté
System info:
Platform Linux-3.10.0-1160.el7.x86_64-x86_64-with-glibc2.17
Python 3.11.3 | packaged by conda-forge | (main, Apr 6 2023, 08:57:19) [GCC 11.3.0]
Executable /home/ma09/.conda/envs/my_mne1.4/bin/python
CPU x86_64 (32 cores)
Memory 251.4 GB
Core
├☑ mne 1.4.0
├☑ numpy 1.24.3 (OpenBLAS 0.3.23 with 32 threads)
├☑ scipy 1.10.1
├☑ matplotlib 3.7.1 (backend=agg)
├☑ pooch 1.7.0
└☑ jinja2 3.1.2
Numerical (optional)
├☑ sklearn 1.2.2
├☑ numba 0.57.0
├☑ nibabel 5.1.0
├☑ nilearn 0.10.1
├☑ dipy 1.7.0
├☑ openmeeg 2.5.6
├☑ pandas 2.0.2
└☐ unavailable cupy
Visualization (optional)
├☑ pyvista 0.39.1 (OpenGL unavailable)
├☑ pyvistaqt 0.0.0
├☑ ipyvtklink 0.2.2
├☑ vtk 9.2.6
├☑ qtpy 2.3.1 (None=None)
├☑ pyqtgraph 0.13.3
├☑ mne-qt-browser 0.0.0
└☐ unavailable ipympl
Ecosystem (optional)
├☑ mne-bids 0.12
├☑ mne-bids-pipeline 1.3.0
└☐ unavailable mne-nirs, mne-features, mne-connectivity, mne-icalabel