Skip to main content

Python Library to Read and Write Surface Files in Freesurfer's TriangularSurface Format

Project description

https://img.shields.io/badge/code%20style-black-000000.svg https://travis-ci.org/fphammerle/freesurfer-surface.svg?branch=master https://coveralls.io/repos/github/fphammerle/freesurfer-surface/badge.svg?branch=master https://img.shields.io/pypi/v/freesurfer-surface.svg https://img.shields.io/pypi/pyversions/freesurfer-surface.svg https://zenodo.org/badge/185943856.svg

Python Library to Read and Write Surface Files in Freesurfer’s TriangularSurface Format

Freesurfer https://surfer.nmr.mgh.harvard.edu/

Install

pip3 install --user freesurfer-surface

Usage

Read Surface File

from freesurfer_surface import Surface

surface = Surface.read_triangular('bert/surf/lh.pial')

for vertex in surface.vertices[:3]:
    print(vertex)

vertex_0 = surface.vertices[0]
print('coordinates of vertex #0:', (vertex_0.right, vertex_0.anterior, vertex_0.superior))

for triangle_index, triangle in enumerate(surface.triangles[:4]):
    print(f'\ntriangle #{triangle_index}:')
    print('vertex indices:', triangle.vertex_indices)
    print('vertex coordinates:')
    for vertex in surface.select_vertices(triangle.vertex_indices):
        print((vertex.right, vertex.anterior, vertex.superior))

Edit Surface File

from freesurfer_surface import Surface, Vertex, Triangle
surface = Surface.read_triangular('bert/surf/lh.pial'))
vertex_a = surface.add_vertex(Vertex(0.0, 0.0, 0.0))
vertex_b = surface.add_vertex(Vertex(1.0, 1.0, 1.0))
vertex_c = surface.add_vertex(Vertex(2.0, 2.0, 2.0))
surface.triangles.append(Triangle((vertex_a, vertex_b, vertex_c)))
surface.write_triangular('somewhere/else/lh.pial')

List Labels in Annotation File

from freesurfer_surface import Annotation

annotation = Annotation.read('tests/subjects/fabian/label/lh.aparc.annot')
for label in annotation.labels.values():
    print(label.index, label.hex_color_code, label.name)

or

$ freesurfer-annotation-labels tests/subjects/fabian/label/lh.aparc.annot
index  color    name
0      #190519  unknown
1      #196428  bankssts
2      #7d64a0  caudalanteriorcingulate
3      #641900  caudalmiddlefrontal
...
33     #4614aa  temporalpole
34     #9696c8  transversetemporal
35     #ffc020  insula

Find Border of Labelled Region

from freesurfer_surface import Surface
surface = Surface.read_triangular('bert/surf/lh.pial'))
surface.load_annotation_file('bert/label/lh.aparc.annot')
region, = filter(lambda l: l.name == 'precentral',
                 annotation.labels.values())
print(surface.find_label_border_polygonal_chains(region))

Tests

pip3 install --user pipenv
git clone https://github.com/fphammerle/freesurfer-surface.git
cd freesurfer-surface
pipenv run pylint freesurfer_surface
pipenv run pytest --cov=freesurfer_surface

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

freesurfer-surface-2.0.0.tar.gz (3.4 MB view details)

Uploaded Source

Built Distribution

freesurfer_surface-2.0.0-py3-none-any.whl (23.1 kB view details)

Uploaded Python 3

File details

Details for the file freesurfer-surface-2.0.0.tar.gz.

File metadata

  • Download URL: freesurfer-surface-2.0.0.tar.gz
  • Upload date:
  • Size: 3.4 MB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/3.3.0 pkginfo/1.4.2 requests/2.25.1 setuptools/52.0.0 requests-toolbelt/0.9.1 tqdm/4.57.0 CPython/3.9.4

File hashes

Hashes for freesurfer-surface-2.0.0.tar.gz
Algorithm Hash digest
SHA256 57f9b5e986a0a2270a1140436764754a7338fc902c81c1cfe3abbb3470e9957a
MD5 bf22f449688b26052eac9a854b5ba59c
BLAKE2b-256 db2f06a0f2812b2894bd37094c8c2eefc7043dc504dcea78706509926f9a6493

See more details on using hashes here.

File details

Details for the file freesurfer_surface-2.0.0-py3-none-any.whl.

File metadata

  • Download URL: freesurfer_surface-2.0.0-py3-none-any.whl
  • Upload date:
  • Size: 23.1 kB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/3.3.0 pkginfo/1.4.2 requests/2.25.1 setuptools/52.0.0 requests-toolbelt/0.9.1 tqdm/4.57.0 CPython/3.9.4

File hashes

Hashes for freesurfer_surface-2.0.0-py3-none-any.whl
Algorithm Hash digest
SHA256 57ad13e7ead5640fc309e1dff94c47d7d546b306edcd244d0232a46650e196b3
MD5 4c9a703bb297368bd8d448d506127844
BLAKE2b-256 916e83692c3af5d6421934d03703dbd1230e574474dafd1c7e30f46d4ad1f2db

See more details on using hashes here.

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page