<gh_stars>1-10
"""
=============================
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 <sphx_glr_auto_tutorials_plot_background_freesurfer.py>`
(https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates) [1]_. 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.

References
----------
.. [1] <NAME>., <NAME>., <NAME>., <NAME>., <NAME>.
       R., <NAME>., <NAME>.
       A Surface-based Analysis of Language Lateralization and Cortical
       Asymmetry. Journal of Cognitive Neuroscience 25(9), 1477-1492, 2013.

.. note:: For a tutorial about morphing see:
          :ref:`ch_morph`.
"""
# Author: <NAME> <<EMAIL>>
#
# License: BSD (3-clause)
import os

import mne
from mne.datasets import sample

print(__doc__)

###############################################################################
# Setup paths

sample_dir_raw = sample.data_path()
sample_dir = os.path.join(sample_dir_raw, 'MEG', 'sample')
subjects_dir = os.path.join(sample_dir_raw, 'subjects')

fname_stc = os.path.join(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:`sphx_glr_auto_tutorials_plot_object_source_estimate.py`).
# This list can either be obtained from
# :class:`mne.SourceSpaces` (src) or from the ``stc`` itself.
#
# Since the default ``spacing`` (resolution of surface mesh) is ``5`` and
# ``subject_to`` is set to 'fsaverage', :class:`mne.SourceMorph` will use
# default ico-5 ``fsaverage`` vertices to morph, which are the special
# values ``[np.arange(10242)] * 2``.
#
# .. note:: This is not generally true for other subjects! The set of vertices
#           used for ``fsaverage`` with ico-5 spacing was designed to be
#           special. ico-5 spacings for other subjects (or other spacings
#           for fsaverage) must be calculated and will not be consecutive
#           integers.
#
# If src was not defined, the morph will actually not be precomputed, because
# we lack the vertices *from* that we want to compute. Instead the morph will
# be set up and when applying it, the actual transformation will be computed on
# the fly.
#
# Initialize SourceMorph for SourceEstimate

morph = mne.compute_source_morph(stc, subject_from='sample',
                                 subject_to='fsaverage',
                                 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)

"""
=============================
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 <sphx_glr_auto_tutorials_plot_background_freesurfer.py>`
(https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates) [1]_. 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.

References
----------
.. [1] <NAME>., <NAME>., <NAME>., <NAME>., <NAME>.
       R., <NAME>., <NAME>.
       A Surface-based Analysis of Language Lateralization and Cortical
       Asymmetry. Journal of Cognitive Neuroscience 25(9), 1477-1492, 2013.

.. note:: For a tutorial about morphing see:
          :ref:`ch_morph`.
"""
# Author: <NAME> <<EMAIL>>
#
# License: BSD (3-clause)
import os

import mne
from mne.datasets import sample

print(__doc__)

###############################################################################
# Setup paths

sample_dir_raw = sample.data_path()
sample_dir = os.path.join(sample_dir_raw, 'MEG', 'sample')
subjects_dir = os.path.join(sample_dir_raw, 'subjects')

fname_stc = os.path.join(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:`sphx_glr_auto_tutorials_plot_object_source_estimate.py`).
# This list can either be obtained from
# :class:`mne.SourceSpaces` (src) or from the ``stc`` itself.
#
# Since the default ``spacing`` (resolution of surface mesh) is ``5`` and
# ``subject_to`` is set to 'fsaverage', :class:`mne.SourceMorph` will use
# default ico-5 ``fsaverage`` vertices to morph, which are the special
# values ``[np.arange(10242)] * 2``.
#
# .. note:: This is not generally true for other subjects! The set of vertices
#           used for ``fsaverage`` with ico-5 spacing was designed to be
#           special. ico-5 spacings for other subjects (or other spacings
#           for fsaverage) must be calculated and will not be consecutive
#           integers.
#
# If src was not defined, the morph will actually not be precomputed, because
# we lack the vertices *from* that we want to compute. Instead the morph will
# be set up and when applying it, the actual transformation will be computed on
# the fly.
#
# Initialize SourceMorph for SourceEstimate

morph = mne.compute_source_morph(stc, subject_from='sample',
                                 subject_to='fsaverage',
                                 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)
============================= 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 <sphx_glr_auto_tutorials_plot_background_freesurfer.py>` (https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates) [1]_. 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.  References ---------- .. [1] <NAME>., <NAME>., <NAME>., <NAME>., <NAME>.        R., <NAME>., <NAME>.        A Surface-based Analysis of Language Lateralization and Cortical        Asymmetry. Journal of Cognitive Neuroscience 25(9), 1477-1492, 2013.  .. note:: For a tutorial about morphing see:           :ref:`ch_morph`. # Author: <NAME> <<EMAIL>> # # License: BSD (3-clause) ############################################################################### # Setup paths ############################################################################### # Load example data # Read stc from file ############################################################################### # Setting up SourceMorph for SourceEstimate # ----------------------------------------- # # In MNE surface source estimates represent the source space simply as # lists of vertices (see # :ref:`sphx_glr_auto_tutorials_plot_object_source_estimate.py`). # This list can either be obtained from # :class:`mne.SourceSpaces` (src) or from the ``stc`` itself. # # Since the default ``spacing`` (resolution of surface mesh) is ``5`` and # ``subject_to`` is set to 'fsaverage', :class:`mne.SourceMorph` will use # default ico-5 ``fsaverage`` vertices to morph, which are the special # values ``[np.arange(10242)] * 2``. # # .. note:: This is not generally true for other subjects! The set of vertices #           used for ``fsaverage`` with ico-5 spacing was designed to be #           special. ico-5 spacings for other subjects (or other spacings #           for fsaverage) must be calculated and will not be consecutive #           integers. # # If src was not defined, the morph will actually not be precomputed, because # we lack the vertices *from* that we want to compute. Instead the morph will # be set up and when applying it, the actual transformation will be computed on # the fly. # # Initialize SourceMorph for SourceEstimate ############################################################################### # 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. ############################################################################### # Plot results # ------------ # Define plotting parameters # As spherical surface # Add title ############################################################################### # As inflated surface # Add title ############################################################################### # 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: