Installing Pick Tracts

Pick Tracts Slicer 4 Module

[Deprecated] Please use the drag-and-drop interface of the Models module in Slicer to create tract hierarchies instead.

This module allows the user to name and group tract clusters. The output is a text file that organizes the atlas clusters into anatomical groups (white matter regions) of interest. This file is used for analysis and visualization of the regions.

NOTE: Currently this module does not export into MRML fiber bundle hierarchy format, which allows measurement of grouped and labeled clusters using the Fiber Tract Measurements Module. The current recommendation is to use the drag-and-drop interface of the Models module in Slicer to create this MRML file, rather than using Pick Tracts. See here: https://github.com/ljod/whitematteranalysis/wiki/Visualization-and-Analysis-of-Clustered-Tracts

Contributors

Lauren O'Donnell

Ruizhi Liao

Install Pick Tracts

• First install Slicer 4 from http://download.slicer.org/
• Install whitematteranalysis from http://ljod.github.io/whitematteranalysis/, in order to get the
• Point Slicer to the PickTracts directory using the following steps.
• Go to Edit->Application Settings. The Settings window will pop up.
• Choose Modules from the menu in the left part of the window.
• Under Additional Module Paths, add the path to the PickTracts directory. (Click the arrow to the right if you don't see an Add button.) This path should be the path on your system to where you installed whitematteranalysis, followed by the path to Pick Tracts: whitematteranalysis/Slicer4/TractCluster/PickTracts
• Slicer will ask to restart in order to find the module.

Use Pick Tracts

• Run Slicer 4.
• Go to Examples->PickTracts in the modules list.
• Load a mrml file (Slicer scene file) produced by whitematteranalysis clustering or atlas building.
• To pick, label, and group tracts, follow the instructions under Help in the PickTracts module.