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2007 AHM Project Half Week

This page presents the work that was done by Nicole Aucoin at the 2007 Project Half Week.

2007 Project Half Week complete list of projects.

4 blocks presented during project week:

For current status on these modules, see Documentation page.


  • MRML Color nodes implemented
  • basic module UI done, display colours with scalar id, names, color box
  • incorporated color node selector in volumes and models GUIs
  • FreeSurfer default Heat, Green/Red look up tables are supported, as well as reading in default labels and annotation labels, and loading color tables from annotation files.
  • Procedural color nodes expanded, support for vtkColorTransferFunction as well as vtkLookupTable in the viewer widget.
  • Scalar overlays supported in the Models GUI, Display tab.
  • TO DO: continue work on UI


  • MRML Node for list implemented, GUI for module refined
  • vtkGlyphSource2D subclassed for Slicer, StarBurst option integrated
  • vtkSlicerGlyphSource2D usable in both the main viewer and in 2D slices
  • 3D glyphs of various types implemented for the 3D viewer
  • S. Pieper linked 2D and 3D fiducials, can drag fiducials in 2D
  • Placing fiducials in the 3D window mostly complete
  • TO DO: Support dragging fiducials in the 3D window


  • MGH ITK Reader ported from NAMIC Sandbox, works as any other volume reader now
  • Slicer 2.x source code ported as a Slicer 3 Library, used in Query Atlas scripts
  • FreeSurfer .W surfaces and CURV surfaces are loadable through the Models GUI
  • FreeSurfer scalar overlays are loadable via the Models Display GUI: thickness, curv, sulc, area, annot, and the new volume encoded scalars in MGH format
  • vtkFSLookupTables integrated into MRML Color Nodes
  • Added support to composite two scalar arrays into one
  • color transfer functions support added to MRML Color Nodes for calculating transfer functions when composite two scalar arrays
  • TODO: other volume format support through the GUI instead of just scriptable, support scalar overlay compositing through the GUI


  • Implemented as a Command Line Module
  • Added option to write out a MRML file with display nodes giving color information (tries to pick a good default color node to get names from)
  • TODO: waiting for support for XML files as input to the CLI modules so can use a defined vtkMRMLColorNode to name models