2010 Winter Project Week Tractography

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  Projects List

Key Investigators

• BWH: Peter Savadjiev, James Malcolm, 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.

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. Savadjiev, Campbell, Pike, Siddiqi. "3D Curve Inference for Diffusion MRI Regularization and Fibre Tractography", MedIA 10(5), p.799-813, 2006.
2. Malcolm, Michailovich, Bouix, Westin, Shenton, Rathi. "A filtered approach to neural tractography using the Watson directional function", MedIA 14(1), p.58-69, 2010.
3. Malcolm, Shenton, Rathi. "Neural tractography using an unscented Kalman filter", IPMI, p.126-138, 2009.