Difference between revisions of "2011 Winter Project Week:TwoTensorTracts"
Line 23: | Line 23: | ||
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 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 | + | 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. |
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. | 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. |
Revision as of 19:01, 10 January 2011
Home < 2011 Winter Project Week:TwoTensorTractsKey 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.
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)
- ITK Module
- Slicer Module
- Built-in
- Extension -- commandline
- Extension -- loadable
- Other (Please specify)
References
- test