Repository: mne-tools/mne-python

Issue:
implement a tutorial on regression based baseline correction based on Alday at el. 2019
from Alday et al. 2019:

> Including the baseline interval as a predictor in a GLM-based statistical approach allows the data to determine how much baseline correction is needed, including both full traditional and no baseline correction as special cases. This reduces the amount of variance in the residual error term and thus has the potential to increase statistical power.



Discussion:

Resolving patch:
diff --git a/tutorials/epochs/15_baseline_regression.py b/tutorials/epochs/15_baseline_regression.py
new file mode 100644
--- /dev/null
+++ b/tutorials/epochs/15_baseline_regression.py
@@ -0,0 +1,285 @@
+# -*- coding: utf-8 -*-
+"""
+.. _ex-baseline-regression:
+
+====================================================================
+Regression-based baseline correction
+====================================================================
+
+This tutorial compares traditional baseline correction (adding or subtracting a
+scalar amount from every timepoint in an epoch) to a regression-based approach
+to baseline correction (which allows the effect of the baseline period to vary
+by timepoint). Specifically, this tutorial follows the method introduced by
+:footcite:t:`Alday2019`.
+
+There are at least two reasons you might consider using regression-based
+baseline correction:
+
+1. Unlike traditional baseline correction, the regression-based approach does
+   not assume that the effect of the baseline is equivalent between different
+   experimental conditions. Thus it is safer against introduced bias.
+
+2. Assuming that pre-trial baseline signal level is mostly determined by slow
+   drifts in the data, the further away (in time) you get from the baseline
+   period, the less likely it is that the signal level is similar in amplitude
+   to the baseline amplitude. Thus using a time-varying baseline correction is
+   less likely to introduce signal distortions / spurious effects in the later
+   spans of long-duration epochs.
+
+One issue that affects both traditional and regression-based baseline
+correction is the question of what time window to choose as the baseline
+window.
+"""
+
+# %%
+
+# Authors: Carina Forster
+# Email: carinaforster0611@gmail.com
+
+# License: BSD-3-Clause
+
+import numpy as np
+
+import mne
+
+# %%
+# Load the data
+# =============
+#
+# We'll start by loading the MNE-Python :ref:`sample dataset <sample-dataset>`
+# and extracting the experimental events to get trial locations and trial
+# types. Since for this tutorial we're only going to look at EEG channels, we
+# can drop the other channel types, to speed things up:
+
+data_path = mne.datasets.sample.data_path()
+raw_fname = data_path / 'MEG' / 'sample' / 'sample_audvis_filt-0-40_raw.fif'
+raw = mne.io.read_raw_fif(raw_fname, preload=True)
+
+events = mne.find_events(raw)
+
+raw.pick_types(meg=False, stim=False, eog=False, eeg=True)
+
+# %%
+# Here we merge visual and auditory events from both hemispheres, and make our
+# ``event_id`` dictionary for use during epoching.
+
+events = mne.merge_events(events, [1, 2], 1)  # auditory events will be "1"
+events = mne.merge_events(events, [3, 4], 2)  # visual events will be "2"
+event_id = {'auditory': 1, 'visual': 2}
+
+
+# %%
+# Preprocessing
+# =============
+#
+# Next we'll define some variables needed to epoch and preprocess the
+# data. We'll be combining left- and right-side stimuli, so we'll look at a
+# single *central* electrode to visualize the difference between auditory and
+# visual trials.
+
+tmin, tmax = -0.2, 0.5
+lowpass, highpass = 40, 0.1
+baseline_tmin, baseline_tmax = None, 0  # None takes the first timepoint
+ch = "EEG 021"
+
+# %%
+# We'll do some standard preprocessing (a bandpass filter) and then epoch
+# the data. Note that we don't baseline correct the epochs (we specify
+# ``baseline=None``); we just minimally clean the data by rejecting channels
+# with very high or low amplitudes.  Note also that we operate on a *copy* of
+# the data so that we can later compare this with traditional baselining.
+
+raw_filtered = raw.copy().filter(highpass, lowpass)
+
+epochs = mne.Epochs(raw_filtered, events, event_id, tmin=tmin, tmax=tmax,
+                    reject=dict(eeg=150e-6), flat=dict(eeg=5e-6),
+                    baseline=None, preload=True)
+
+
+# %%
+# Traditional baselining
+# ----------------------
+#
+# First let's baseline correct the data the traditional way. We average epochs
+# within each condition, and subtract the condition-specific baseline
+# separately for auditory and visual trials.
+
+baseline = (baseline_tmin, baseline_tmax)
+trad_aud = epochs['auditory'].average().apply_baseline(baseline)
+trad_vis = epochs['visual'].average().apply_baseline(baseline)
+
+# %%
+# Regression-based baselining
+# ---------------------------
+#
+# Now let's try out the regression-based baseline correction approach. We'll
+# use :func:`mne.stats.linear_regression`, which needs a *design matrix* to
+# represent the regression predictors. We'll use four predictors: one for each
+# experimental condition, one for the effect of baseline, and one that is an
+# interaction between the baseline and one of the conditions (to account for
+# any heterogeneity of the effect of baseline between the two conditions). Here
+# are the first two:
+
+aud_predictor = epochs.events[:, 2] == epochs.event_id['auditory']
+vis_predictor = epochs.events[:, 2] == epochs.event_id['visual']
+
+# %%
+# The baseline predictor is a bit trickier to compute: we'll find the average
+# value within the baseline period *separately for each epoch*, and use that
+# value as our (trial-level) predictor.  Here, since we're focused on one
+# particular channel, we'll use the baseline value *in that channel* as our
+# predictor, but depending on your research question you may want to do this
+# seaprately for each channel or combine information across channels.
+
+baseline_predictor = (
+    epochs.copy()
+          .crop(*baseline)
+          .pick_channels([ch])
+          .get_data()     # convert to NumPy array
+          .mean(axis=-1)  # average across timepoints
+          .squeeze()      # only 1 channel, so remove singleton dimension
+)
+baseline_predictor *= 1e6  # convert V → μV
+
+# %%
+# Note that we converted *just the predictor* (not the epochs data) from Volts
+# to microVolts. This is done for regression-model-fitting purposes (very small
+# values can make model fitting unstable).
+#
+# Now we can set up the design matrix, stacking the 1-D predictors as rows,
+# then transposing with ``.T`` to make them columns. Combining them into one
+# :func:`~numpy.array` will also automatically convert the
+# :class:`boolean <bool>` ``aud_predictor`` and ``vis_predictor`` into
+# ones and zeros:
+
+design_matrix = np.vstack([aud_predictor,
+                           vis_predictor,
+                           baseline_predictor,
+                           baseline_predictor * vis_predictor]).T
+
+# %%
+# Finally we fit the regression model:
+
+reg_model = mne.stats.linear_regression(epochs, design_matrix,
+                                        names=["auditory", "visual",
+                                               "baseline",
+                                               "baseline:visual"])
+
+# %%
+# The function returns a dictionary of ``mne.stats.regression.lm`` objects,
+# which are each a :func:`~collections.namedtuple` with the various estimated
+# values stored as if it were an :class:`~mne.Evoked` object. Let's inspect it:
+
+print(reg_model.keys())
+print(f"model attributes: {reg_model['auditory']._fields}")
+print('values are stored in Evoked objects:')
+print(reg_model['auditory'].t_val)
+
+# %%
+# Plot the baseline regressor
+# ===========================
+#
+# First let's look at the estimated effect of the baseline period. What we care
+# about is the ``beta`` values, which tell us how strongly predictive the
+# baseline value is at each timepoint. The model will estimate its
+# effectiveness *for every channel* but since we used only one channel to form
+# our baseline predictor, let's examine how it looks for that channel only.
+# We'll add a horizontal line at β=1 to represent traditional baselining, where
+# the effect is assumed to be constant across timepoints:
+
+effect_of_baseline = reg_model['baseline'].beta
+effect_of_baseline.plot(picks=ch, hline=[1.], units=dict(eeg=r'$\beta$ value'),
+                        titles=dict(eeg=ch), selectable=False)
+
+# %%
+# Unsurprisingly, the trend is that the farther away in time we get from the
+# baseline period, the weaker the predictive value of the baseline amplitude
+# becomes. Put another way, early time points (in this data) should be more
+# strongly baseline-corrected than later time points.
+#
+# Plot the ERPs
+# =============
+#
+# Now let's look at the ``beta`` values for the two
+# conditions (``auditory`` and ``visual``): these are the coefficients that
+# represent the "pure" influence of the experimental stimuli on the signal,
+# after taking into account the (time-varying!) effect of the baseline. We'll
+# plot them together, side-by-side with the traditional baseline approach:
+
+reg_aud = reg_model['auditory'].beta
+reg_vis = reg_model['visual'].beta
+
+kwargs = dict(picks=ch, show_sensors=False, truncate_yaxis=False)
+mne.viz.plot_compare_evokeds(dict(auditory=trad_aud, visual=trad_vis),
+                             title="Traditional", **kwargs)
+mne.viz.plot_compare_evokeds(dict(auditory=reg_aud, visual=reg_vis),
+                             title="Regression-based", **kwargs)
+
+# %%
+# They look pretty similar, but there are some subtle differences in how far
+# apart the two conditions are (e.g., around 400-500 ms).
+#
+# Plot the scalp topographies and difference waves
+# ================================================
+#
+# Now let's compare the
+# scalp topographies for the traditional and regression-based approach. We'll
+# do this by computing the difference between conditions:
+
+diff_traditional = mne.combine_evoked([trad_aud, trad_vis], weights=[1, -1])
+diff_regression = mne.combine_evoked([reg_aud, reg_vis], weights=[1, -1])
+
+# %%
+# Before we plot, let's make sure we get the same color scale for both figures:
+
+vmin = min(diff_traditional.get_data().min(),
+           diff_regression.get_data().min()) * 1e6
+vmax = max(diff_traditional.get_data().max(),
+           diff_regression.get_data().max()) * 1e6
+topo_kwargs = dict(vmin=vmin, vmax=vmax, ch_type='eeg',
+                   times=np.linspace(0.05, 0.45, 9))
+
+diff_traditional.plot_topomap(title="Traditional", **topo_kwargs)
+
+# %%
+diff_regression.plot_topomap(title="Regression-based", **topo_kwargs)
+
+# %%
+# We can see that the regression-based approach shows *stronger* difference
+# between conditions early on (around 100-150 ms) and *weaker* differences
+# later (around 250-350 ms, and again around 450 ms). This is also reflected in
+# the difference waves themselves: notice how the regression-based difference
+# wave is *further from zero* around 150 ms but *closer to zero* around 250-350
+# ms.
+
+title = "Difference in evoked potential (auditory minus visual)"
+fig = mne.viz.plot_compare_evokeds(dict(Traditional=diff_traditional,
+                                        Regression=diff_regression),
+                                   title=title, **kwargs)
+
+# %%
+# Examine the interaction term
+# ============================
+#
+# Finally, let's look at the interaction term from the regression model. This
+# tells us whether the effect of the baseline period is different in the visual
+# trials versus its effect in the auditory trials. Here we'll add a horizontal
+# line at zero, indicating the assumption that there ought to be no difference
+# (i.e., baselines should not be systematically higher in one type of trial,
+# and there should not be a difference in how long the effect of the baseline
+# persists through time in each type of trial).
+
+interaction_effect = reg_model['baseline:visual'].beta
+interaction_effect.plot(picks=ch, hline=[0.], units=dict(eeg=r'$\beta$ value'),
+                        titles=dict(eeg=ch), selectable=False)
+
+
+# %%
+# Indeed, the interaction beta weights are rather small and seem to fluctuate
+# randomly around zero, suggesting that there is no systematic difference in
+# the effect of the baseline on our two trial types.
+
+# %%
+# References
+# ==========
+# .. footbibliography::


Test patch: