2011 Winter Project Week:TwoTensorTracts

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  Projects List

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  Example whole brain clustering result.

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  Example two-tensor tractography result.

Key Investigators

• BWH: Lauren O'Donnell, Yogesh Rathi, C-F Westin

Objective

To test 2-tensor tractography in Slicer3/standalone and hook it up to full-brain clustering pipelines.

Approach, Plan

Our goals for the project week are to update clustering I/O to read tracts as a single large polydata file per subject, and to produce output in Slicer3 MRML format.

I could use help regarding the best way to have Slicer3 run a script to produce MRML. My matlab code writes a script that currently is run by Slicer2, in order to append polydata into clusters, and produce a MRML file pointing to the clusters, that includes colors derived from matlab clustering.

The next step is to ascertain what needs to be done to visualize/label the clusters in slicer3 or 4. This is in order to make atlases or study a particular tract. The old slicer2 interface allowed interactive selection of clusters (show/hide selected, and show/hide labeled or unlabeled) and anatomical naming/labeling.

Progress

Attempted to compile standalone and module 2-tensor Kalman filter tractography on a Mac. I could use help here regarding python compilation and installation of blas/lapack -- this module code has not been compiled on a Mac before.

Installed Slicer3/4. Tested installation of clustering.

Delivery Mechanism

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

1. ITK Module
2. Slicer Module
   1. Built-in
   2. Extension -- commandline
   3. Extension -- loadable
3. Other (Please specify)

References

• test