2010 Winter Project Week Tractography

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  Projects List

Key Investigators

• BWH: James Malcolm, Peter Savadjiev, Yogesh Rathi, C-F Westin

Objective

Integrate recent methods for filtered tractography into Slicer3 using Python.

Plan

Implement various local models and filtering techniques. Support both region-of-interest and fiducial seeding. Support both interactive and batch processing. Picking fibers and moving them between polydata structures.

Progress

We have MATLAB implementations of various local models (single-tensor, two-tensor, Watson functions, weighted mixtures of these, etc.) and various model-based filters (Kalman, unscented Kalman, particle, etc.). We have begun converting these to NumPy/Python as well as the additional infrastructure for performing tractography within Slicer.

1. Malcolm, Michailovich, Bouix, Westin, Shenton, Rathi. "A filtered approach to neural tractography using the Watson directional function", MedIA 14(1), p.58-69, 2010.
2. Malcolm, Shenton, Rathi. "Neural tractography using an unscented Kalman filter", IPMI, p.126-138, 2009.
3. Savadjiev, Zucker, Siddiqi. "On the Differential Geometry of 3D Flow Patterns: Generalized Helicoids and Diffusion MRI Analysis", ICCV 2007