freesurfer-surface ================== .. image:: https://img.shields.io/badge/code%20style-black-000000.svg :target: https://github.com/psf/black .. 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