Dear All,
Iโm trying to run the MNE Sample data demo with MNE-BIDS-Pipeline.
I get the following error, saying that the file does not start with a file id tag:
(/cognestic/mne) cognestic@labQLFR95:~/Desktop/cognestic/notebooks$ mne_bids_pipeline --config=demo_config.py
โโโโโโโโโโฌ Welcome aboard MNE-BIDS-Pipeline! ๏ โโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโ
โ16:07:00โ ๏ Using configuration: demo_config.py
โโโโโโโโโโด
โโโโโโโโโโฌ init/_01_init_derivatives_dir โโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโ
โ16:07:00โ โ
Output directories already exist โฆ
โโโโโโโโโโด done (1s)
โโโโโโโโโโฌ init/_02_find_empty_room โโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโ
โ16:07:00โ โ
sub-01 run-01 Computation unnecessary (cached) โฆ
โโโโโโโโโโด done (1s)
โโโโโโโโโโฌ preprocessing/_01_data_quality โโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโ
โ16:07:02โ โณ๏ธ sub-01 run-01 Finding flat channels and noisy channels using Maxwell filtering.
โ16:07:02โ โ sub-01 run-01 A critical error occurred. The error message was: file '/home/cognestic/mne_data/ds000248/sub-01/meg/sub-01_task-audiovisual_run-01_meg.fif' does not start with a file id tag
Aborting pipeline run. The traceback is:
File "/cognestic/mne/lib/python3.12/site-packages/mne_bids_pipeline/steps/preprocessing/_01_data_quality.py", line 87, in assess_data_quality
auto_scores = _find_bads_maxwell(
^^^^^^^^^^^^^^^^^^^
File "/cognestic/mne/lib/python3.12/site-packages/mne_bids_pipeline/steps/preprocessing/_01_data_quality.py", line 175, in _find_bads_maxwell
raw = import_experimental_data(
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/cognestic/mne/lib/python3.12/site-packages/mne_bids_pipeline/_import_data.py", line 386, in import_experimental_data
raw = _load_data(cfg=cfg, bids_path=bids_path_in)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/cognestic/mne/lib/python3.12/site-packages/mne_bids_pipeline/_import_data.py", line 227, in _load_data
raw = read_raw_bids(
^^^^^^^^^^^^^^
File "<decorator-gen-387>", line 12, in read_raw_bids
File "/cognestic/mne/lib/python3.12/site-packages/mne_bids/read.py", line 857, in read_raw_bids
raw = _read_raw(
^^^^^^^^^^
File "/cognestic/mne/lib/python3.12/site-packages/mne_bids/read.py", line 72, in _read_raw
raw = reader(raw_path, allow_maxshield, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/cognestic/mne/lib/python3.12/site-packages/mne/io/fiff/raw.py", line 537, in read_raw_fif
return Raw(
^^^^
File "<decorator-gen-266>", line 12, in __init__
File "/cognestic/mne/lib/python3.12/site-packages/mne/io/fiff/raw.py", line 105, in __init__
raw, next_fname, buffer_size_sec = self._read_raw_file(
^^^^^^^^^^^^^^^^^^^^
File "<decorator-gen-267>", line 12, in _read_raw_file
File "/cognestic/mne/lib/python3.12/site-packages/mne/io/fiff/raw.py", line 197, in _read_raw_file
ff, tree, _ = fiff_open(fname, preload=whole_file)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "<decorator-gen-7>", line 12, in fiff_open
File "/cognestic/mne/lib/python3.12/site-packages/mne/_fiff/open.py", line 134, in fiff_open
return _fiff_open(fname, fid, preload)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/cognestic/mne/lib/python3.12/site-packages/mne/_fiff/open.py", line 153, in _fiff_open
raise ValueError(f"{prefix} start with a file id tag")
I used a fresh copy of the ds00248 dataset and the config file supplied in the demo.
I used mne-bids-pipeline version 1.8.0 as that is the version bundled with the latest mne-python, but I also tested it with version 1.9.0 (everything else unchanged) and it throws the same error. Detailed system info below.
Could you please look into this and help me get the pipeline running?
Many thanks,
Mรกtรฉ
System info:
Platform Linux-6.5.0-1023-azure-x86_64-with-glibc2.35
Python 3.12.2 | packaged by conda-forge | (main, Feb 16 2024, 20:50:58) [GCC 12.3.0]
Executable /cognestic/mne/bin/python3.12
CPU x86_64 (4 cores)
Memory 15.6 GB
Core
โโ mne 1.7.1 (latest release)
โโ numpy 1.26.4 (OpenBLAS 0.3.27 with 4 threads)
โโ scipy 1.13.1
โโ matplotlib 3.8.4Installed qt5 event loop hook.
(backend=QtAgg)
Numerical (optional)
โโ sklearn 1.5.0
โโ numba 0.59.1
โโ nibabel 5.2.1
โโ nilearn 0.10.4
โโ dipy 1.9.0
โโ openmeeg 2.5.11
โโ pandas 2.2.2
โโ h5io 0.2.3
โโ h5py 3.11.0
โโ unavailable cupy
Visualization (optional)
โโ pyvista 0.43.9 (OpenGL 4.5 (Core Profile) Mesa 23.2.1-1ubuntu3.1~22.04.2 via llvmpipe (LLVM 15.0.7, 256 bits))
โโ pyvistaqt 0.11.0
โโ vtk 9.2.6
โโ qtpy 2.4.1 (PyQt5=5.15.8)
โโ ipympl 0.9.4
โโ pyqtgraph 0.13.7
โโ mne-qt-browser 0.6.3
โโ ipywidgets 8.1.3
โโ trame_client 3.1.0
โโ trame_server 3.0.1
โโ trame_vtk 2.8.9
โโ trame_vuetify 2.6.0
Ecosystem (optional)
โโ mne-bids 0.15.0
โโ mne-nirs 0.6.0
โโ mne-features 0.3
โโ mne-connectivity 0.7.0
โโ mne-icalabel 0.6.0
โโ mne-bids-pipeline 1.8.0
โโ neo 0.13.0
โโ eeglabio 0.0.2-4
โโ edfio 0.4.2
โโ mffpy 0.9.0
โโ pybv 0.7.5