mne-tools / mne-tools/mne-python
ValueError in mne.viz.plot_sensors_connectivit
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Description
Hi, I was trying to learn https://mne.tools/stable/auto_examples/connectivity/plot_sensor_connectivity.html#sphx-glr-auto-examples-connectivity-plot-sensor-connectivity-py.I change the method to 'coh', aka the coherence, and I've got this error:
ValueError: zero-size array to reduction operation maximum which has no identity
And here is my code
import mne
from mne import io
from mne.connectivity import spectral_connectivity
from mne.datasets import sample
from mne.viz import plot_sensors_connectivity
data_path = sample.data_path()
raw_fname = data_path + '/MEG/sample/sample_audvis_filt-0-40_raw.fif'
event_fname = data_path + '/MEG/sample/sample_audvis_filt-0-40_raw-eve.fif'
raw = io.read_raw_fif(raw_fname)
events = mne.read_events(event_fname)
raw.info['bads'] += ['MEG 2443']
picks = mne.pick_types(raw.info, meg='grad', eeg=False, stim=False, eog=True,
exclude='bads')
event_id, tmin, tmax = 3, -0.2, 1.5 # need a long enough epoch for 5 cycles
epochs = mne.Epochs(raw, events, event_id, tmin, tmax, picks=picks,
baseline=(None, 0), reject=dict(grad=4000e-13, eog=150e-6))
fmin, fmax = 3., 9.
sfreq = raw.info['sfreq'] # the sampling frequency
tmin = 0.0 # exclude the baseline period
epochs.load_data().pick_types(meg='grad') # just keep MEG and no EOG now
con, freqs, times, n_epochs, n_tapers = spectral_connectivity(
epochs, method='coh', mode='multitaper', sfreq=sfreq, fmin=fmin, fmax=fmax,
faverage=True, tmin=tmin, mt_adaptive=False, n_jobs=1)
plot_sensors_connectivity(epochs.info, con[:, :, 0])
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Research direction
Start with the connectivity example at plot_sensor_connectivity.html and reproduce the reported ValueError using the supplied sample-data script. Trace the interaction between spectral_connectivity with method='coh' and plot_sensors_connectivity, then verify that the example completes and produces the sensor-connectivity plot without the zero-size array error.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data-visualization
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100