surface watershed

Usage

Run using mc_script surface watershed after installation or using ~ndcn0236/bin/mc_script surface watershed on jalapeno.

Import in python using from mcutils.scripts.surface import watershed

Documentation

Creates maps of gyri or sulci using watershed algorithm

The watershed algorithm sorts all vertices based on sulcal depth (or some other metric) and then visits them one by one:

  • if none of the neighbour have been visited yet (i.e., the vertex is a local minimum) the vertex is given a new label

  • if only one neighbour has a label (or all neighbours have the same label), the vertex is given that label

  • if different neigbours of the vertex have different labels one of the following two actions is taken:

    • if either of the masks is below the minumum size (in mm^2) or below the minimum depth (i.e., the difference between the lowest value of the metric and the value in the current vertex) then the two parcels are merged (and the vertex is given the value of the new parcel)

    • otherwise both parcels are kept separate and the vertex is identified as being on the ridge between these parcels.

Functions

run(surface, depth[, min_depth, min_size, …])

Runs watershed on the graph generated on the surface

run_nparcels(surface, depth, nparcels[, …])

Returns a parcellation with requested number of parcels based on watershed algorithm

CLI interface

add_to_parser(parser)

Creates the parser of the command line arguments

run_from_args(args)

Runs the script based on a Namespace containing the command line arguments