write.fs.surface.gii: Write mesh to file in GIFTI surface format

In neuroconductor/freesurferformats: Read and Write 'FreeSurfer' Neuroimaging File Formats

Description

Write vertex coordinates and vertex indices defining faces to a file in GIFTI surface format. For a subject (MRI image pre-processed with FreeSurfer) named 'bert', an example file would be 'bert/surf/lh.white.asc'.

Usage

write.fs.surface.gii(filepath, vertex_coords, faces)

Arguments

filepath	string. Full path to the output surface file, should end with '.asc', but that is not enforced.
vertex_coords	n x 3 matrix of doubles. Each row defined the x,y,z coords for a vertex.
faces	n x 3 matrix of integers. Each row defined the 3 vertex indices that make up the face. WARNING: Vertex indices should be given in R-style, i.e., the index of the first vertex is 1. However, they will be written in FreeSurfer style, i.e., all indices will have 1 substracted, so that the index of the first vertex will be zero.

Value

string the format that was written. One of "tris" or "quads". Currently only triangular meshes are supported, so always 'tris'.

See Also

Other mesh functions: faces.quad.to.tris(), read.fs.surface.asc(), read.fs.surface.bvsrf(), read.fs.surface.geo(), read.fs.surface.gii(), read.fs.surface.ico(), read.fs.surface.obj(), read.fs.surface.off(), read.fs.surface.ply(), read.fs.surface.vtk(), read.fs.surface(), read.mesh.brainvoyager(), read_nisurfacefile(), read_nisurface(), write.fs.surface.asc(), write.fs.surface.byu(), write.fs.surface.mz3(), write.fs.surface.vtk(), write.fs.surface()

Other gifti writers: write.fs.annot.gii(), write.fs.label.gii(), write.fs.morph.gii()

Examples

    # Read a surface from a file:
    surface_file = system.file("extdata", "lh.tinysurface",
     package = "freesurferformats", mustWork = TRUE);
    mesh = read.fs.surface(surface_file);

    # Now save it:
    write.fs.surface.gii(tempfile(fileext=".gii"), mesh$vertices, mesh$faces);

neuroconductor/freesurferformats documentation built on May 20, 2021, 3:15 p.m.