Difference between revisions of "2011 Winter Project Week:TwoTensorTracts"

From NAMIC Wiki
Jump to: navigation, search
Line 21: Line 21:
 
<h3>Approach, Plan</h3>
 
<h3>Approach, Plan</h3>
  
Our approach
+
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. 
  
Our plan for the project week is ...
+
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.
  
 
</div>
 
</div>
Line 30: Line 32:
  
 
<h3>Progress</h3>
 
<h3>Progress</h3>
 
+
Attempted to compile standalone and module 2-tensor Kalman filter tractography on a Mac. 
 
+
Installed Slicer3/4.
 +
Tested installation of clustering.
  
 
</div>
 
</div>

Revision as of 18:57, 10 January 2011

Home < 2011 Winter Project Week:TwoTensorTracts

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. 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