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https://github.com/NeuroanatomyAndConnectivity/surfdist
For calculating exact geodesic distances on cortical surface meshes
https://github.com/NeuroanatomyAndConnectivity/surfdist
Last synced: 3 months ago
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For calculating exact geodesic distances on cortical surface meshes
- Host: GitHub
- URL: https://github.com/NeuroanatomyAndConnectivity/surfdist
- Owner: NeuroanatomyAndConnectivity
- License: mit
- Created: 2015-10-23T23:24:28.000Z (over 8 years ago)
- Default Branch: master
- Last Pushed: 2023-11-13T15:14:39.000Z (7 months ago)
- Last Synced: 2024-03-17T22:50:13.197Z (3 months ago)
- Language: Python
- Size: 1.42 MB
- Stars: 44
- Watchers: 5
- Forks: 24
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
- License: LICENSE.txt
Lists
- awesome-stars - surfdist
README
surfdist
========
[![Build Status](https://travis-ci.com/NeuroanatomyAndConnectivity/surfdist.svg?branch=master)](https://travis-ci.com/NeuroanatomyAndConnectivity/surfdist)Calculate the exact geodesic distance on a triangular surface mesh using the [gdist package](https://pypi.python.org/pypi/gdist/), which is based on the [c++ library](https://code.google.com/p/geodesic/).
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()