From Slicer Wiki
Revision as of 19:26, 26 January 2013 by Reckbo2 (talk | contribs)
Jump to: navigation, search
Home < Documentation < 4.2 < Modules < UKFTractography

Introduction and Acknowledgements

This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the NA-MIC website.
Author: Yogesh Rathi, Ph.D, Psychiatry Neuroimaging Laboratory, Brigham & Women's Hospital
Contact: FIRSTNAME LASTNAME, <email></email>

Isomics, Inc. <- Replace this logo with yours  
Surgical Planning Laboratory (SPL) <-Replace this logo with yours  

Module Description

We present a framework which uses an unscented Kalman filter for performing tractography. At each point on the fiber the most consistent direction is found as a mixture of previous estimates and of the local model.

It is very easy to expand the framework and to implement new fiber representations for it. Currently it is possible to tract fibers using two different 1-, 2-, or 3-tensor methods. Both methods use a mixture of Gaussian tensors. One limits the diffusion ellipsoids to a cylindrical shape (the second and third eigenvalue are assumed to be identical) and the other one uses a full tensor representation.

Authors: Yogesh Rathi (, Stefan Lienhard, Yinpeng Li, Martin Styner, Ipek Oguz, Yundi Shi, Christian Baumgartner (, Ryan Eckbo

Use Cases

  • 1-Tensor tractography
  • 1-Tensor tractography with free water
  • 2-Tensor tractography
  • 2-Tensor tractography with free water



Panels and their use


Similar Modules



Reference for 2-tensor tractography:

Reference for 1-tensor and 2-tensor + free-water:

  • C. Baumgartner, O. Michailovich, O. Pasternak, S. Bouix, J. Levitt, ME Shenton, C-F Westin, Y. Rathi,

"A unified tractography framework for comparing diffusion models on clinical scans": in Workshop on computational diffusion MRI, 2012.

Information for Developers