Get ROI Voxel Mask¶
Get proportion of each voxel that exists within a named ROI (this constitutes a probability map for the ROI, with values ranging from 0-1). Plot this probablistic roi mask onto a flatmap.
In order for this to work, the specified ROI must exist in the overlays.svg file in the pycortex filestore for this subject.
Found 100.00% of EBA Cutting 0 overlapping voxels (should be < ~50) Generating a flatmap cache
import cortex import matplotlib.pyplot as plt subject = "S1" xfm = "fullhead" roi = "EBA" # Get the map of which voxels are inside of our ROI roi_masks = cortex.utils.get_roi_masks(subject, xfm, roi_list=[roi], gm_sampler='cortical-conservative', # Select only voxels mostly within cortex split_lr=False, # No separate left/right ROIs threshold=None, # Leave roi mask values as probabilites / fractions return_dict=True ) # Plot the mask for one ROI onto a flatmap roi_data = cortex.Volume(roi_masks[roi], subject, xfm, vmin=0, # This is a probability mask, so only vmax=1, # so scale btw zero and one cmap="inferno", # For pretty ) cortex.quickflat.make_figure(roi_data, thick=1, # select a single depth (btw white matter & pia) sampler='nearest', # no interpolation with_curvature=True, with_colorbar=True, ) plt.show()
Total running time of the script: ( 0 minutes 9.668 seconds)