Jadrian Miles: New page: Tubegen is a rather broken "Jack of all trades and master of none." We'd like to split it apart into several programs that each do something simple. The [[Job Jar/Streamline statistics p...

2011-02-15T14:10:06Z

New page: Tubegen is a rather broken "Jack of all trades and master of none." We'd like to split it apart into several programs that each do something simple. The [[Job Jar/Streamline statistics p...

New page

Tubegen is a rather broken "Jack of all trades and master of none." We'd like to split it apart into several programs that each do something simple. The [[Job Jar/Streamline statistics program|streamline stats program]] and culling program accomplish two important steps, but there are a couple left:

=== 1. Seed Generation ===
Generate a set of random seed points at a given density. Input: seed density in seeds / mm^3, image file (in NIfTI or MRIimage, from which to read dimensions) or image dimensions in mm. Output: list of seed coordinates (one seed per line) written to a file (or standard output if no file is specified).

=== 2. Streamline Generation ===
Read in a list of seed points and generate streamlines from them, terminating the advection process according to a threshold criterion and a curvature criterion. Input: list of seed coordinates (from a file, or standard input if no file is specified), a diffusion tensor image (as NIfTI or MRIimage), an optional curvature criterion (with a default value), an optional scalar image (as NIfTI or MRIimage), and an optional scalar threshold. Output: a curve collection, either as a trackvis .trk file, a .ccf file (your format), or in CCF format to standard output if no filename is specified.

Job Jar/Tubegen replacement - Revision history

Jadrian Miles: New page: Tubegen is a rather broken "Jack of all trades and master of none." We'd like to split it apart into several programs that each do something simple. The [[Job Jar/Streamline statistics p...