Slicer3:ColorsFiducialsFreesurferModelmaker

2007 AHM Project Half Week

2007 Project Half Week complete list of projects.

4 blocks presented during project week:

• Colors
• Fiducials
• FreeSurfer
• ModelMaker

Colors

• 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

Fiducials

• 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

FreeSurfer

• 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

ModelMaker

• 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