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# -*- coding: utf-8 -*-
"""
.. _ex-morph-surface:
=============================
Morph surface source estimate
=============================
This example demonstrates how to morph an individual subject's
:class:`mne.SourceEstimate` to a common reference space. We achieve this using
:class:`mne.SourceMorph`. Pre-computed data will be morphed based on
a spherical representation of the cortex computed using the spherical
registration of :ref:`FreeSurfer <tut-freesurfer-mne>`
(https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates)
:footcite:`GreveEtAl2013`. This
transform will be used to morph the surface vertices of the subject towards the
reference vertices. Here we will use 'fsaverage' as a reference space (see
https://surfer.nmr.mgh.harvard.edu/fswiki/FsAverage).
The transformation will be applied to the surface source estimate. A plot
depicting the successful morph will be created for the spherical and inflated
surface representation of ``'fsaverage'``, overlaid with the morphed surface
source estimate.
.. note:: For background information about morphing see :ref:`ch_morph`.
"""
# Author: Tommy Clausner <tommy.clausner@gmail.com>
#
# License: BSD-3-Clause
# %%
import mne
from mne.datasets import sample
print(__doc__)
# %%
# Setup paths
data_path = sample.data_path()
sample_dir = data_path / 'MEG' / 'sample'
subjects_dir = data_path / 'subjects'
fname_src = subjects_dir / 'sample' / 'bem' / 'sample-oct-6-src.fif'
fname_fwd = sample_dir / 'sample_audvis-meg-oct-6-fwd.fif'
fname_fsaverage_src = (subjects_dir / 'fsaverage' / 'bem' /
'fsaverage-ico-5-src.fif')
fname_stc = sample_dir / 'sample_audvis-meg'
# %%
# Load example data
# Read stc from file
stc = mne.read_source_estimate(fname_stc, subject='sample')
# %%
# Setting up SourceMorph for SourceEstimate
# -----------------------------------------
#
# In MNE, surface source estimates represent the source space simply as
# lists of vertices (see :ref:`tut-source-estimate-class`).
# This list can either be obtained from :class:`mne.SourceSpaces` (src) or from
# the ``stc`` itself. If you use the source space, be sure to use the
# source space from the forward or inverse operator, because vertices
# can be excluded during forward computation due to proximity to the BEM
# inner skull surface:
src_orig = mne.read_source_spaces(fname_src)
print(src_orig) # n_used=4098, 4098
fwd = mne.read_forward_solution(fname_fwd)
print(fwd['src']) # n_used=3732, 3766
print([len(v) for v in stc.vertices])
# %%
# We also need to specify the set of vertices to morph to. This can be done
# using the ``spacing`` parameter, but for consistency it's better to pass the
# ``src_to`` parameter.
#
# .. note::
# Since the default values of :func:`mne.compute_source_morph` are
# ``spacing=5, subject_to='fsaverage'``, in this example
# we could actually omit the ``src_to`` and ``subject_to`` arguments
# below. The ico-5 ``fsaverage`` source space contains the
# special values ``[np.arange(10242)] * 2``, but in general this will
# not be true for other spacings or other subjects. Thus it is recommended
# to always pass the destination ``src`` for consistency.
#
# Initialize SourceMorph for SourceEstimate
src_to = mne.read_source_spaces(fname_fsaverage_src)
print(src_to[0]['vertno']) # special, np.arange(10242)
morph = mne.compute_source_morph(stc, subject_from='sample',
subject_to='fsaverage', src_to=src_to,
subjects_dir=subjects_dir)
# %%
# Apply morph to (Vector) SourceEstimate
# --------------------------------------
#
# The morph will be applied to the source estimate data, by giving it as the
# first argument to the morph we computed above.
stc_fsaverage = morph.apply(stc)
# %%
# Plot results
# ------------
# Define plotting parameters
surfer_kwargs = dict(
hemi='lh', subjects_dir=subjects_dir,
clim=dict(kind='value', lims=[8, 12, 15]), views='lateral',
initial_time=0.09, time_unit='s', size=(800, 800),
smoothing_steps=5)
# As spherical surface
brain = stc_fsaverage.plot(surface='sphere', **surfer_kwargs)
# Add title
brain.add_text(0.1, 0.9, 'Morphed to fsaverage (spherical)', 'title',
font_size=16)
# %%
# As inflated surface
brain_inf = stc_fsaverage.plot(surface='inflated', **surfer_kwargs)
# Add title
brain_inf.add_text(0.1, 0.9, 'Morphed to fsaverage (inflated)', 'title',
font_size=16)
# %%
# Reading and writing SourceMorph from and to disk
# ------------------------------------------------
#
# An instance of SourceMorph can be saved, by calling
# :meth:`morph.save <mne.SourceMorph.save>`.
#
# This method allows for specification of a filename under which the ``morph``
# will be save in ".h5" format. If no file extension is provided, "-morph.h5"
# will be appended to the respective defined filename::
#
# >>> morph.save('my-file-name')
#
# Reading a saved source morph can be achieved by using
# :func:`mne.read_source_morph`::
#
# >>> morph = mne.read_source_morph('my-file-name-morph.h5')
#
# Once the environment is set up correctly, no information such as
# ``subject_from`` or ``subjects_dir`` must be provided, since it can be
# inferred from the data and use morph to 'fsaverage' by default. SourceMorph
# can further be used without creating an instance and assigning it to a
# variable. Instead :func:`mne.compute_source_morph` and
# :meth:`mne.SourceMorph.apply` can be
# easily chained into a handy one-liner. Taking this together the shortest
# possible way to morph data directly would be:
stc_fsaverage = mne.compute_source_morph(stc,
subjects_dir=subjects_dir).apply(stc)
# %%
# For more examples, check out :ref:`examples using SourceMorph.apply
# <sphx_glr_backreferences_mne.SourceMorph.apply>`.
#
#
# References
# ----------
# .. footbibliography::
|
