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README.rst

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')

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('\ntriangle #{}:'.format(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
~~~~~~~~~~~~~~~~~

.. 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