Slicer3:ColorsFiducialsFreesurferModelmaker

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:

• Colors
• Fiducials
• FreeSurfer
• ModelMaker

For current status on these modules, see Documentation page.

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