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- freesurfer-surface
- ==================
- .. image:: https://travis-ci.org/fphammerle/freesurfer-surface.svg?branch=master
- :target: https://travis-ci.org/fphammerle/freesurfer-surface
- .. image:: https://coveralls.io/repos/github/fphammerle/freesurfer-surface/badge.svg?branch=master
- :target: https://coveralls.io/github/fphammerle/freesurfer-surface?branch=master
- .. image:: https://img.shields.io/pypi/v/freesurfer-surface.svg
- :target: https://pypi.org/project/freesurfer-surface/#history
- .. image:: https://img.shields.io/pypi/pyversions/freesurfer-surface.svg
- :target: https://pypi.org/project/freesurfer-surface/
- .. image:: https://zenodo.org/badge/185943856.svg
- :target: https://zenodo.org/badge/latestdoi/185943856
- Python Library to Read and Write Surface Files in Freesurfer’s
- TriangularSurface Format
- Freesurfer https://surfer.nmr.mgh.harvard.edu/
- Install
- -------
- .. code:: sh
- pip3 install --user freesurfer-surface
- Usage
- -----
- Read Surface File
- ~~~~~~~~~~~~~~~~~
- .. code:: python
- from freesurfer_surface import Surface
- surface = Surface.read_triangular('bert/surf/lh.pial')
- print('some vertices:', surface.vertices[:3])
- vertex_0 = surface.vertices[0]
- print('coordinates of vertex #0:', (vertex_0.right, vertex_0.anterior, vertex_0.superior))
- print('some triangles:', surface.triangles[:4])
- triangle_0 = surface.triangles[0]
- print('vertices of triangle #0:', triangle_0)
- print('vertex coordinates of triangle #0:', surface.select_vertices(triangle_0.vertex_indices))
- Edit Surface File
- ~~~~~~~~~~~~~~~~~
- .. code:: python
- 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
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- .. code:: python
- 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
- .. code:: sh
- $ 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
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- .. code:: python
- 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
- -----
- .. code:: sh
- 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
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