Documentation/4.6/Modules/UKFTractography

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Introduction and Acknowledgements

:Title: :Author(s)/Contributor(s): :License: :Acknowledgements: Contact: <email>slicer-users@bwh.harvard.edu</email> Website: https://github.com/pnlbwh/ukftractography Website: http://slicerdmri.github.io/

SlicerDMRI   NAC   Arcuate fasciculus (AF) tract in the setting of edema [Chen et al, 2015]   Corpus callosum (CC) tract

Module Description

For additional references, please see below (References section).

Use Cases

By default, this module uses a tensor model (either one or two tensors). The default tensor model is a cylinder: both smaller eigenvalues are equal. The NODDI model can also be used.

• 1-Tensor tractography
• 1-Tensor tractography with free water
• 2-Tensor tractography
• 2-Tensor tractography with free water
• Neurite orientation dispersion and density imaging (NODDI)

Tutorials

• UKF Tractography tutorial: https://www.slicer.org/slicerWiki/index.php/Documentation/4.5/Training#UKF

Panels and their use

Parameters:

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     * ': 
     
       ** ': 
       
        *** ': 
       
     
   
 

List of parameters generated transforming this XML file using this XSL file. To update the URL of the XML file, edit this page.

Similar Modules

• Tractography Seeding
• Tractography ROI Seeding
• Diffusion Tensor Estimation

References

• Reference for 2-tensor tractography:
  • Malcolm, J.G., Shenton, M.E. and Rathi, Y., 2010. Filtered multitensor tractography. IEEE transactions on medical imaging, 29(9), pp.1664-1675.
• Reference for 1-tensor and 2-tensor + free-water:
  • Baumgartner C, Michailovich O, Levitt J, Pasternak O, Bouix S, Westin C, Rathi Y. A unified tractography framework for comparing diffusion models on clinical scans. In Computational Diffusion MRI Workshop of MICCAI, Nice 2012 (pp. 27-32).
• Reference for using UKF in clinical imaging data from tumor patients with edema:
  • Chen Z, Tie Y, Olubiyi O, Rigolo L, Mehrtash A, Norton I, Pasternak O, Rathi Y, Golby AJ, O'Donnell LJ. Reconstruction of the arcuate fasciculus for surgical planning in the setting of peritumoral edema using two-tensor unscented Kalman filter tractography. NeuroImage: Clinical. 2015 Dec 31;7:815-22.
• Reference for NODDI UKF tractography:
  • Reddy, C.P. and Rathi, Y., 2016. Joint Multi-Fiber NODDI Parameter Estimation and Tractography Using the Unscented Information Filter. Frontiers in Neuroscience, 10.

Information for Developers

• https://github.com/pnlbwh/ukftractography
• https://www.nitrc.org/projects/ukftractography