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For calculating exact geodesic distances on cortical surface meshes

Project description

surfdist

Build Status

Calculate the exact geodesic distance on a triangular surface mesh using the gdist package, which is based on the c++ library.

Installation

pip install surfdist

Example

import nibabel as nib
import numpy as np
import matplotlib.pyplot as plt
import os
import surfdist as sd
from surfdist import viz, load, utils, analysis

# calculate and display distance from central sulcus at each node:
cmap = 'coolwarm'
base_dir = '/Applications/freesurfer/subjects/'
surf = nib.freesurfer.read_geometry(os.path.join(base_dir, 'bert/surf/lh.pial'))
cort = np.sort(nib.freesurfer.read_label(os.path.join(base_dir, 'bert/label/lh.cortex.label')))
sulc = nib.freesurfer.read_morph_data(os.path.join(base_dir, 'bert/surf/lh.sulc'))

# load central sulcus nodes
src  = sd.load.load_freesurfer_label(os.path.join(base_dir, 'bert/label/lh.aparc.a2009s.annot'), 'S_central', cort)

# calculate distance
dist = sd.analysis.dist_calc(surf, cort, src)

# visualize
plot_med = sd.viz.viz(surf[0], surf[1], dist, bg_map=sulc, bg_on_stat=True, cmap=cmap)
plot_lat = sd.viz.viz(surf[0], surf[1], dist, azim=180, bg_map=sulc, bg_on_stat=True, cmap=cmap)

# Calculate distances on native surface and display on fsaverage
fsa4 = nib.freesurfer.read_geometry(os.path.join(base_dir,'fsaverage4/surf/lh.sphere.reg'))[0]
fsa4_sulc=nib.freesurfer.read_morph_data(os.path.join(base_dir, 'fsaverage4/surf/lh.sulc'))
native = nib.freesurfer.read_geometry(os.path.join(base_dir, 'bert/surf/lh.sphere.reg'))[0]
idx_fsa4_to_native = sd.utils.find_node_match(fsa4, native)[0]

surf_fsa4 = nib.freesurfer.read_geometry(os.path.join(base_dir, 'fsaverage4/surf/lh.pial'))
plot_fsa4_med = sd.viz.viz(surf_fsa4[0], surf_fsa4[1], dist[idx_fsa4_to_native], bg_map=fsa4_sulc, bg_on_stat=True, cmap=cmap)
plot_fsa4_lat = sd.viz.viz(surf_fsa4[0], surf_fsa4[1], dist[idx_fsa4_to_native], azim=180, bg_map=fsa4_sulc, bg_on_stat=True, cmap=cmap)

plt.show()

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