Map from Volume to Vertex Data

In order to move from Volume data to Vertex data, you start with data from voxels and then create a cortex.Volume object. Then, you get a mapper to go between voxels and vertices for the specific subject and transform you are working with. Pass the voxel volume through the mapper and you get out a vertex mapping of that data. You can plot both of these as you normally would.

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Out:

Failed to get connection
** (inkscape:5131): CRITICAL **: 01:26:57.515: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed
** (inkscape:5131): CRITICAL **: 01:26:57.515: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed
** (inkscape:5131): CRITICAL **: 01:26:57.515: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed
Generating a flatmap cache
Failed to get connection
** (inkscape:5134): CRITICAL **: 01:26:59.615: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed
** (inkscape:5134): CRITICAL **: 01:26:59.615: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed
** (inkscape:5134): CRITICAL **: 01:26:59.615: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed

import cortex
import cortex.polyutils
import numpy as np
np.random.seed(1234)
import matplotlib.pyplot as plt

subject = 'S1'
xfm = 'fullhead'

# First create example voxel data for this subject and transform
voxel_data = np.random.randn(31, 100, 100)
voxel_vol = cortex.Volume(voxel_data, subject, xfm)

# Then we have to get a mapper from voxels to vertices for this transform
mapper = cortex.get_mapper(subject, xfm, 'line_nearest', recache=True)

# Just pass the voxel data through the mapper to get vertex data
vertex_map = mapper(voxel_vol)

# You can plot both as you would normally plot Volume and Vertex data
cortex.quickshow(voxel_vol)
plt.show()
cortex.quickshow(vertex_map)
plt.show()