freesurfer-surface 0.1.0

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

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

compatible with Freesurfer’s MRISwriteTriangularSurface() https://github.com/freesurfer/freesurfer/blob/release_6_0_0/include/mrisurf.h#L1281 https://github.com/freesurfer/freesurfer/blob/release_6_0_0/utils/mrisurf.c https://raw.githubusercontent.com/freesurfer/freesurfer/release_6_0_0/utils/mrisurf.c

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

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(‘bert/label/lh.aparc.annot’) >>> for label in annotation.labels.values(): >>> print(label.index, label.hex_color_code, label.name)

Find Border of Labelled Region >>> 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))