""" ============================ Plot Intracranial Electrodes ============================ This notebook demonstrates calculating anatomical information about intracranial electrodes and plotting on the Freesurfer average brain. """ # Author: Gavin Mischler # # License: MIT import numpy as np import matplotlib.pyplot as plt import naplib as nl from naplib.localization import Brain from naplib.visualization import plot_brain_elecs, plot_brain_overlay ############################################################################### # Load freesurfer fsaverage data if we don't have it import os import mne os.makedirs('./fsaverage', exist_ok=True) mne.datasets.fetch_fsaverage('./fsaverage/') ############################################################################### # Create a brain with the pial surface for computing metrics brain = Brain('pial', subject_dir='./fsaverage/').split_hg('midpoint').split_stg().simplify_labels() # Specify the coordinates of 30 electrodes in fsaverage space coords = np.array([[-47.281147 , 17.026093 , -21.833099 ], [-48.273964 , 16.155487 , -20.162935 ], [-51.101261 , 13.711058 , -16.258459 ], [-55.660889 , 9.761111 , -12.340655 ], [-58.733326 , 6.046287 , -9.626602 ], [-60.749279 , 2.233287 , -8.044459 ], [-61.26712 , -1.939675 , -8.582445 ], [-63.686226 , -10.447982 , -0.445693 ], [-63.453224 , -9.826311 , 1.095302 ], [-48.792809 , 15.73144 , -19.34193 ], [-51.336754 , 13.27527 , -15.57861 ], [-53.301971 , 11.016301 , -12.48259 ], [-55.044659 , 9.894337 , -11.228349 ], [-57.597462 , 6.753941 , -8.082416 ], [-60.594891 , 2.579503 , -6.884331 ], [-63.078999 , -8.770401 , -1.878142 ], [-67.419235 , -26.153931 , -1.260003 ], [-60.28742599, -11.71243477, 5.62593937], [-63.12403107, -12.37896156, 4.09772062], [ 64.44213867, -3.16063929, -6.95104313], [ 61.58537674, -23.53317833, -3.20349312], [ 69.31034851, -18.18317795, 1.97798777], [ 69.0439682 , -18.64465904, 1.2625511 ], [ 68.32962799, -20.90372849, -0.25190961], [ 59.79437256, -23.76178932, -3.52095652], [-56.57900238, -9.23060513, -7.33194447], [-58.861763 , -11.2859602 , -6.18047237], [-61.13874054, -11.35863781, -4.49999475], [-60.82435989, -8.91696072, -3.20156574], [-61.00576019, -7.45676041, -3.06485367]]) isleft = coords[:,0]<0 ############################################################################### # Get anatomical labels for each electrode anatomical_labels = brain.annotate_coords(coords, isleft) print(anatomical_labels) ############################################################################### # Compute the distance of each electrode from posteromedial HG along the # cortical surface dist_from_HG = brain.distance_from_region(coords, isleft, region='pmHG', metric='surf') print(dist_from_HG) ############################################################################### # Smoothly interpolate values over the brain's surface from electrodes # As an example, we will use the y coordinate of the electrode values_per_electrode = coords[:,1] - coords[:,1].min() # Interpolate onto only the temporal lobe, using the 5 nearest neighbor interpolation with # a maximum distance of 10mm brain.interpolate_electrodes_onto_brain(coords, values_per_electrode, isleft, roi='temporal', k=5, max_dist=10) # Plot the overlay for just the left hemisphere fig, axes = plot_brain_overlay(brain, cmap='Reds', view='lateral', figsize=(12,6), hemi='lh') plt.show() ############################################################################### # Create a brain with the inflated surface for plotting brain = Brain('inflated', subject_dir='./fsaverage/').split_hg('midpoint').split_stg().simplify_labels() ############################################################################### # Plot electrode locations with matplotlib, and color the electrodes # by their distance from HG fig, axes = plot_brain_elecs(brain, coords, isleft, values=dist_from_HG, hemi='lh', view='lateral') plt.show() ############################################################################### # Plot electrodes with an interactive plotly figure, and instead of coloring them by a value, we # will color them by a custom color for each electrode. # Some common use-cases for this might be to color electrodes based on the identity of the subject # they came from when pooling electrodes, or by a categorical variable. In this case, we color # them by the anatomical labels they were assigned to (black for posterior STG and red for middle STG) colors = ['k' if lab == 'pSTG' else 'r' for lab in anatomical_labels] fig, axes = plot_brain_elecs(brain, coords, isleft, colors=colors, backend='plotly') fig.write_html("interactive_brain_plot.html") # save as an interactive html plot fig.show() # show the interactive plot in the notebook ############################################################################### # Color certain brain regions by their label brain.paint_overlay('mSTG', -3) brain.paint_overlay('pSTG', 3) brain.paint_overlay('MTG', 1) fig, axes = plot_brain_overlay(brain, view='lateral') plt.show() ############################################################################### # Plot default Destrieux Atlas region labels overlaid on the brain brain = Brain('pial', subject_dir='./fsaverage/') brain.lh.overlay = brain.lh.labels brain.rh.overlay = brain.rh.labels fig, axes = plot_brain_overlay(brain, cmap='tab20') plt.show() ############################################################################### # Load and plot Glasser Atlas region labels overlaid on the brain brain = Brain('pial', atlas='HCPMMP1', subject_dir='./fsaverage/') brain.lh.overlay = brain.lh.labels brain.rh.overlay = brain.rh.labels fig, axes = plot_brain_overlay(brain, cmap='prism') plt.show()