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%matplotlib inline
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
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.
.. [1] Greve D. N., Van der Haegen L., Cai Q., Stufflebeam S., Sabuncu M. R., Fischl B., Brysbaert M. A Surface-based Analysis of Language Lateralization and Cortical Asymmetry. Journal of Cognitive Neuroscience 25(9), 1477-1492, 2013.
For a tutorial about morphing see: `sphx_glr_auto_tutorials_plot_morph_stc.py`.
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# Author: Tommy Clausner <tommy.clausner@gmail.com>
#
# License: BSD (3-clause)
import os
import mne
from mne.datasets import sample
print(__doc__)
Setup paths
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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
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# Read stc from file
stc = mne.read_source_estimate(fname_stc, subject='sample')
In MNE surface source estimates represent the source space simply as
lists of vertices (see
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
.
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
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morph = mne.compute_source_morph(stc, subject_from='sample',
subject_to='fsaverage',
subjects_dir=subjects_dir)
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stc_fsaverage = morph.apply(stc)
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# 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
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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)
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:
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stc_fsaverage = mne.compute_source_morph(stc,
subjects_dir=subjects_dir).apply(stc)