8.2.14. Loading and plotting of a cortical surface atlas

The Destrieux parcellation (Destrieux et al, 2010) in fsaverage5 space as distributed with Freesurfer is used as the chosen atlas.

The nilearn.plotting.plot_surf_roi function is used to plot the parcellation on the pial surface.

See Plotting brain images for more details.

NOTE: Example needs matplotlib version higher than 1.3.1.

8.2.14.1. References

Destrieux et al, (2010). Automatic parcellation of human cortical gyri and sulci using standard anatomical nomenclature. NeuroImage, 53, 1. URL http://dx.doi.org/10.1016/j.neuroimage.2010.06.010.

8.2.14.2. Data fetcher

# Retrieve destrieux parcellation in fsaverage5 space from nilearn
from nilearn import datasets

destrieux_atlas = datasets.fetch_atlas_surf_destrieux()

# The parcellation is already loaded into memory
parcellation = destrieux_atlas['map_left']

# Retrieve fsaverage5 surface dataset for the plotting background. It contains
# the surface template as pial and inflated version and a sulcal depth maps
# which is used for shading
fsaverage = datasets.fetch_surf_fsaverage5()

# The fsaverage dataset contains file names pointing to the file locations
print('Fsaverage5 pial surface of left hemisphere is at: %s' %
      fsaverage['pial_left'])
print('Fsaverage5 inflated surface of left hemisphere is at: %s' %
      fsaverage['infl_left'])
print('Fsaverage5 sulcal depth map of left hemisphere is at: %s' %
      fsaverage['sulc_left'])

Out:

Fsaverage5 pial surface of left hemisphere is at: /home/varoquau/nilearn_data/fsaverage5/pial.left.gii
Fsaverage5 inflated surface of left hemisphere is at: /home/varoquau/nilearn_data/fsaverage5/pial_inflated.left.gii
Fsaverage5 sulcal depth map of left hemisphere is at: /home/varoquau/nilearn_data/fsaverage5/sulc.left.gii

8.2.14.3. Visualization

# Display Destrieux parcellation on fsaverage5 pial surface using nilearn
from nilearn import plotting

plotting.plot_surf_roi(fsaverage['pial_left'], roi_map=parcellation,
                       hemi='left', view='lateral',
                       bg_map=fsaverage['sulc_left'], bg_on_data=True,
                       darkness=.5, cmap='gist_ncar')
../../_images/sphx_glr_plot_surf_atlas_001.png

Display Destrieux parcellation on inflated fsaverage5 surface

plotting.plot_surf_roi(fsaverage['infl_left'], roi_map=parcellation,
                       hemi='left', view='lateral',
                       bg_map=fsaverage['sulc_left'], bg_on_data=True,
                       darkness=.5, cmap='gist_ncar')
../../_images/sphx_glr_plot_surf_atlas_002.png

Display Destrieux parcellation with different views: posterior

plotting.plot_surf_roi(fsaverage['infl_left'], roi_map=parcellation,
                       hemi='left', view='posterior',
                       bg_map=fsaverage['sulc_left'], bg_on_data=True,
                       darkness=.5, cmap='gist_ncar')
../../_images/sphx_glr_plot_surf_atlas_003.png

Display Destrieux parcellation with different views: ventral

plotting.plot_surf_roi(fsaverage['infl_left'], roi_map=parcellation,
                       hemi='left', view='ventral',
                       bg_map=fsaverage['sulc_left'], bg_on_data=True,
                       darkness=.5, cmap='gist_ncar')
plotting.show()
../../_images/sphx_glr_plot_surf_atlas_004.png

Total running time of the script: ( 0 minutes 1.949 seconds)

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