Modules:Modelmaker-Documentation

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The Model Maker Module

The Modelmaker is used to create 3D surface models from segmented image data, called label maps. Label maps can be the result of automated segmentation or interactive editing. The model maker is a pipeline of algorithms that start from the input label map, creates a binary label map with just the label(s) of interest set to 1, everything else to 0, generates a marching cubes model, runs triangle reduction and triangle smoothing algorithms. The pipeline was optimized for 1mm brain MRI data. For other geometries, adjustments of the parameters might be necessary. The model maker is compiled as both a command line executable passed arguments via the command line, and as a binary plug in that communicates through shared memory with Slicer3. The automatically created GUI, found by clickign on the Modules menu, Model Generation category, has the following elements:

• Input/Output:
  • The Input Volume drop down menu is populated with the label map volumes that are present in the scene
  • Models are imported into Slicer under a model hierarchy node, and their colors are set by the color table associated with the input label map volume. The model hierarchy node must be created before running the model maker, by selecting Create New ModelHierarchy from the Models drop down menu.
• Create Multiple:
  • If you specify a list of Labels, it will override any start/end label settings. If you click Generate All it will over ride the list of lables and any start/end label settings.
  • If you want to create all models that correspond to all values in a labelmap volume, click the Generate All Models and Joint Smoothing boxes
• Model Maker Parameters:
  • You can set the number of smoothing iterations, target reduction in number of polygons (decimal percentage). Use 0 and 1 if you wish no smoothing nor decimation.
  • You can set the flags to split normals or generate point normals in this pane as well.
  • You can save a copy of the models after intermediate steps (marching cubes, smoothing, and decimation if not joint smoothing, otherwise just after decimation); these models are not saved in the mrml file, turn off deleting temporary files first in the tcl window: [$::slicer3::CommandLineModuleGUI_Model_Maker GetLogic] DeleteTemporaryFilesOff
• Anatomical Information:
  • Here you can specify an external file linking label values with anatomical names.

This was the original method of linking label map values to resultant model colors and names, but it has been superceded by an internal linkage between the input label map volume and it's color node. If you wish to specify a file for a volume node that does not have a color node associated with it, a sample can be found in . It must be a comma separated file, extension .csv, in the format

 anatomyName1,label1
 anatomyName2,label2

where anatomyName is a string, and label is an integer. If the volume node has a color node associated with it, that will override the anatomy label file.