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Mention gotchas in dipole orientation tutorial. Fix figures.
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wmvanvliet committed Nov 12, 2024
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23 changes: 20 additions & 3 deletions tutorials/inverse/35_dipole_orientations.py
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tutorial, we will look at the various options available to restrict the
orientation of the dipoles and the impact on the resulting source estimate.
.. warning::
A common "gotcha!" is that by default, dipole orientation information is discarded
in the source estimate. Only the magnitude of the activity is retained. This means
that by default, the source-level values are always positive. This has some
implications that may not be immediately obvious:
* Averaging across source estimated epochs does not produce a source estimated
evoked response. Since values are always positive, noise does not "cancel out".
This means the default settings are probably not suitable for things like
performing linear regression or computing correlations across epochs in source
space.
* Oscillatory signals are distorted, as for example a sine wave will become a series
of bumps. Hence, frequency analysis in source space is not meaningful when using
the default settings.
See :ref:`inverse_orientation_constraints` for related information.
"""

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fig=fig,
)

mne.viz.set_3d_view(figure=fig, azimuth=180, distance=0.25)
mne.viz.set_3d_view(figure=fig, azimuth=180, distance=0.1, focalpoint="auto")

# %%
# .. _plot_dipole_orientations_fixed_orientations:
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fig=fig,
)

mne.viz.set_3d_view(figure=fig, azimuth=180, distance=0.1)
mne.viz.set_3d_view(figure=fig, azimuth=180, distance=0.1, focalpoint="auto")

# %%
# Restricting the dipole orientations in this manner leads to the following
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fig=fig,
)

mne.viz.set_3d_view(figure=fig, azimuth=180, distance=0.1)
mne.viz.set_3d_view(figure=fig, azimuth=180, distance=0.1, focalpoint="auto")

# %%
# When computing the source estimate, the activity at each of the three dipoles
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