surfdist
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()
1 maintainer
Metadata
1 maintainer
Release files for surfdist 0.15.5
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| surfdist-0.15.5.tar.gz | 1.2 MB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| surfdist-0.15.5-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 1.2 MB
Release files / surfdist-0.15.5.tar.gz
| Download URL | surfdist-0.15.5.tar.gz |
|---|---|
| Size | 1.2 MB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
b48731996a97f83042d7640d3f35e72ffd4f039f0a9761f729bc23d694ef60a7
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twine/3.2.0 pkginfo/1.5.0.1 requests/2.24.0 setuptools/49.2.0 requests-toolbelt/0.9.1 tqdm/4.48.0 CPython/3.7.3
|
Release files / surfdist-0.15.5-py3-none-any.whl
| Download URL | surfdist-0.15.5-py3-none-any.whl |
|---|---|
| Size | 10.2 kB |
| Tags | Python 3 |
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| Uploaded via |
twine/3.2.0 pkginfo/1.5.0.1 requests/2.24.0 setuptools/49.2.0 requests-toolbelt/0.9.1 tqdm/4.48.0 CPython/3.7.3
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