DT-MRI BWH, MIT Carl-Fredrik Westin, Lauren O’Donnell, Raul San-Jose, Ola Friman, Gordon Kindlmann, William Wells, Sylvain Bouix, Marek Kubicki,

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Presentation transcript:

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

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

What we use 3D Slicer:DTMRI module New documentation http://www.na-mic.org/Wiki/index.php/Slicer:DTMRI (Michelle Perry, UCSD) Splenium of the corpus callosum interconnecting different regions: occipital lobes (green), temporal lobes (red) and thalamus (blue).

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

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

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

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

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

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

Lauren O’Donnell

Lauren O’Donnell

Lauren O’Donnell

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

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

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

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

http://lmi.bwh.harvard.edu

- 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