1. DT-MRI BWH, MIT
Carl-Fredrik Westin, Lauren O’Donnell, Raul San-Jose, Ola Friman, Gordon Kindlmann, William Wells, Sylvain Bouix, Marek Kubicki, …
Laboratory of Mathematics in Imaging

2. DT-MRI Experts at Snowbird
Photo: Sylvain Bouix

3. DT-MRI at BWH and MIT What we use Where standardization is needed
What we can contribute with

4. What we use 3D Slicer:DTMRI module New documentation
(Michelle Perry, UCSD)
Splenium of the corpus callosum interconnecting different regions: occipital lobes (green), temporal lobes (red) and thalamus (blue).

5. DT-MRI Module: New Developments
Interface and Acquisition Protocols
Support of different acquisition protocols
Extendible from interface
Multiple Gradients
Support for more than 6 gradients DWI
Display of ODFs
Display using super-quadrics

6. ODFs in Slicer
J. Snyder, R. San-Jose
D. Tuch, CF Westin

7. Superquadric Glyphs Color-coded fiber directions in canine heart
Gordon Kindlmann

8. DT-MRI Module: Bsplines, Runge-Kutta 4,5
Tractography
ITK B-spline interpolation
Runge-Kutta 4,5
Maxime Boucher

9. DT-MRI Module: Registration
Tensor Registration
Rigid registration
Non-rigid registration (Multi-channel Demon’s Algorithm)
Matthan Caan

10. Tract Clustering in Slicer
Slicer output images (3 slides)
Input region and tract paths
3 Clusters
6 Clusters
Implementation Details
Work in progress
Lauren O’Donnell

11. Lauren O’Donnell

12. Lauren O’Donnell

13. Lauren O’Donnell

14. Implementation Details
Implemented in VTK/ITK
vtkTractShapeFeatures
Compares paths based on shape
Currently uses features from Brun and Westin
vtkNormalizedCuts
Normalized Cuts segmentation algorithm
Cluster based on shape similarity matrix
vnl for eigenvector calculation
ITK K-means
Lauren O’Donnell

15. Work in Progress Add shape features
Hausdorff distance (suggested by Corouge and Gerig)
Higher-order moments
Work on shape similarity vs location tradeoff
Lauren O’Donnell

16. Where standardization is needed
Coordinate systems !!
File formats on disk (raster data, fibers tracts, …)
Internal data structures (ITK, VTK, Matlab)
Readers and Writers between platforms
Data and procedures for testing Readers and Writers

17. What we can contribute with
Nrrd file format
Gordon Kindlmann
Sylvain Bouix, Nrrd format of Stuctural and DTI data from Brockton VA/Harvard
Readers and writers for 3D Slicer
Raul San-Jose
Lauren O’Donnell

19. - END - Reminder: Call for Papers
Special issue in Signal Processing on
Tensor Signal Processing
Deadline for manuscript submission: March 1, 2005
Editors:
Juan Ruiz-Alzola
Carl-Fredrik Westin