Voxel distance from surfaceΒΆ

The utility function get_vox_dist returns the distance from each voxel in some space to the nearest vertex on the given surface. This function is used for generating ROI masks, cortical masks, etc.

plot voxel distance from surface

Out:

<matplotlib.colorbar.Colorbar object at 0x7f226d1b91d0>

import cortex
import matplotlib.pyplot as plt

# get distance to nearest point on the mid-cortical (fiducial) surface from each
# voxel in the functional space for subject 'S1' and the transform 'fullhead'
dist, argdist = cortex.get_vox_dist(subject='S1',
                                    xfmname='fullhead',
                                    surface='fiducial')

# dist contains the distance from each voxel to the nearest vertex
# dist.shape = (31, 100, 100) <-- the same size as the functional volume

# argdist contains the index of the nearest vertex to each voxel
# argdist.shape = (31, 100, 100) <-- the same size as the functional volume

# let's visualize the distance field using the mosaic function
cortex.mosaic(dist, cmap=plt.cm.plasma)
plt.colorbar(label='mm from surface')

Total running time of the script: ( 0 minutes 4.373 seconds)

Gallery generated by Sphinx-Gallery