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DT-MRI BWH, MIT

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 http://lmi.bwh.harvard.edu. DT-MRI Experts at Snowbird. Photo: Sylvain Bouix.

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DT-MRI BWH, MIT

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  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 http://lmi.bwh.harvard.edu

  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 http://www.na-mic.org/Wiki/index.php/Slicer:DTMRI (Michelle Perry, UCSD)

  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 http://teem.sourceforge.net/nrrd/namic-format.html • Sylvain Bouix, Nrrd format of Stuctural and DTI data from Brockton VA/Harvard http://www.na-mic.org/Wiki/index.php/DataRepository • Readers and writers for 3D Slicer • Raul San-Jose • Lauren O’Donnell

  18. http://lmi.bwh.harvard.edu

  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

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