MNE-BIDS-Pipeline ICA step critical error

💬 Support & Discussions
1

Hi,

I’m getting a critical error from mne_bids_pipeline at the ICA stage:

[18:03:15] \u2502 \u274c preprocessing/_05a_run_ica sub-90 A critical error occurred. The error message was: attempt to get argmax of an empty sequence

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 264, in wrapper
    out_files = memorized_func(*args, **kwargs)

  File "/home/ma09/.conda/envs/my_mne1.3/lib/python3.10/site-packages/joblib/memory.py", line 594, in __call__
    return self._cached_call(args, kwargs)[0]

  File "/home/ma09/.conda/envs/my_mne1.3/lib/python3.10/site-packages/joblib/memory.py", line 537, in _cached_call
    out, metadata = self.call(*args, **kwargs)

  File "/home/ma09/.conda/envs/my_mne1.3/lib/python3.10/site-packages/joblib/memory.py", line 779, in call
    output = self.func(*args, **kwargs)

  File "/home/ma09/.conda/envs/my_mne1.3/lib/python3.10/site-packages/mne_bids_pipeline/steps/preprocessing/_05a_run_ica.py", line 299, in run_ica
    ecg_epochs = make_ecg_epochs(

  File "/home/ma09/.conda/envs/my_mne1.3/lib/python3.10/site-packages/mne_bids_pipeline/steps/preprocessing/_05a_run_ica.py", line 131, in make_ecg_epochs
    ecg_epochs = create_ecg_epochs(raw, baseline=(None, -0.2), tmin=-0.5, tmax=0.5)

  File "<decorator-gen-430>", line 12, in create_ecg_epochs

  File "/home/ma09/.conda/envs/my_mne1.3/lib/python3.10/site-packages/mne/preprocessing/ecg.py", line 346, in create_ecg_epochs
    events, _, _, ecg = find_ecg_events(

  File "<decorator-gen-429>", line 12, in find_ecg_events

  File "/home/ma09/.conda/envs/my_mne1.3/lib/python3.10/site-packages/mne/preprocessing/ecg.py", line 202, in find_ecg_events
    max_idx = (ends - onsets).argmax()

ValueError: attempt to get argmax of an empty sequence

It seems that there are no ecg epochs found.

I’m using v1.1.0 of mne_bids_pipeline
The rest of the 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

In my config file I set ICA for artefact removal

spatial_filter: Optional[Literal["ssp", "ica"]] = 'ica'

The rest of the settings for ICA are default.

Could anyone please help?

Many thanks,
Máté

2

do you have an ECG channel in your dataset? if so is your ECG channel clean?

Alex

4

Hi Alex,

Thanks for your response. It seems that I haven’t properly set up my environment before running the pipeline. After setting up everyting properly, the pipeline ran without an error.

Best wishes,
Máté

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