Welcome to documentation for gyral_structure!¶
Describes white matter structure as a vector field. This vector field defines at every point the local fibre orientation and density.
This vector field is defined as the sum of basis functions (defined in
gyral_structure.basis).The coefficients of these basis functions are found by minimizing any cost function (see
gyral_structure.cost).These cost functions generally require the vector field to be evaluated in certain voxels or vertices. These requests are handled by
gyral_structure.request.Finally the algorithm used to compute this vector field is defined by
gyral_structure.algorithm(e.g. cpu or gpu, pre-compute matrix or not).Once the best-fit coefficients have been found streamlines can be computed using
gyral_structure.streamline.
You can view the code at https://git.fmrib.ox.ac.uk/ndcn0236/gyral_structure
Documentation overview¶
- Tutorial
- gyral_structure API
- gyral_structure.basis: defining the basis functions
- gyral_structure.cost package: defining the cost function
- Scripts included in gyral_structure
- gs_mask: Creates a mask of the gyral white matter
- gs_fit: Fits vector field inside gyral white matter
- gs_deform_surface: Moves white/gray matter boundary to deep white matter
- gs_dyad_vol: Evaluates vector field fibre density and orientation in a volume
- gs_dyad_surf: Evaluates vector field fibre density and orientation on a surface
- gs_track: Streamline tractography through vector field
- gyral_structure.algorithm: how to compute the cost function
- gyral_structure.cuda: GPU support
- gyral_structure.request: define which voxels/vertices to evaluate
- gyral_structure.streamline: streamline tractography through vector field
- gyral_structure.utils: several utilities