TubeTK/Documentation/InteractivePDFSegmenter

Documentation

TODO: insert algorithm description here

Tutorial

Tutorial Data

• The 2D brain image used in this example is distributed as part of Slicer4, and is located in Slicer4/Testing/Data/Input/brainSliceDOUBLE.mha

Tutorial Steps

1. Load brainSliceDOUBLE.mha:
   • File -> Add Volume
2. Open the Interactive PDF Segmenter module
3. Set the input and output volumes
   • Input Volume 1: brainSliceDOUBLE
   • Input Volume 2 (optional): None
   • Input Volume 3 (optional): None
   • Output Volume: Create new volume
     • Creates a new volume called "Volume": this will hold the final segmentation
4. Set the view layout to "Red slice only"
5. Create the label map roughly outlining the structures to be segmented and the background
   • Label Map: Create new volume
     • Creates a new volume called "Volume1": this will hold the input label map
   • A small version of Slicer's Editor module is embedded into the Interactive PDF Segmenter
   • Create a label map roughly outlining the structures of interest and the background by using the paint, erase and threshold functions
     • Click on the "Paint" button to begin editing
     • Use a different label color for each structure of interest: choose the label by clicking the colored push button
     • Create a label for the background as well
   • In the following example, green represents gray matter, yellow represents white matter, and brown represents the background