Closed mvdoc closed 3 months ago
These new functions can be used to project data from the volume to any arbitrary surface via a combination of pycortex mappers and mri_surf2surf. The projection deals with nans similar to quickshow and nanproject=True.
mri_surf2surf
nanproject=True
Example code:
import cortex from cortex.mapper import vol2surf import numpy as np subject = ... # anonymized xfm = ... # anonymized vol = cortex.Volume.random(subject, xfm, mask="thick") mask = cortex.db.get_mask(subject, xfm) data = vol.data[mask] data[np.random.randn(*data.shape) > 0] = np.nan new_volume = cortex.Volume(data, subject, xfm, mask="thick") surface = cortex.Vertex(vol2surf(data, subject, xfm), subject) fsaverage = cortex.Vertex(vol2surf(data, subject, xfm, target_surface="fsaverage"), "fsaverage") fig = cortex.quickshow(new_volume, with_colorbar=False, with_curvature=True, with_rois=False, with_labels=False, nanmean=False,) fig.suptitle("volume, nanmean=False", fontsize=24) fig = cortex.quickshow(new_volume, with_colorbar=False, with_curvature=True, with_rois=False, with_labels=False, nanmean=True,) fig.suptitle("volume, nanmean=True", fontsize=24) fig = cortex.quickshow(surface, with_colorbar=False, with_curvature=True, with_rois=False, with_labels=False,) fig.suptitle("vol2surf", fontsize=24) fig = cortex.quickshow(fsaverage, with_colorbar=False, with_curvature=True, with_rois=False, with_labels=False,) fig.suptitle("fsaverage", fontsize=24)
Outputs:
These new functions can be used to project data from the volume to any arbitrary surface via a combination of pycortex mappers and
mri_surf2surf
. The projection deals with nans similar to quickshow andnanproject=True
.Example code:
Outputs: