2011 Summer Project Week Integrate BRAINSCut into Slicer3

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Integrate BRAINSCut into Slicer3

Key Investigators

  • University of Iowa: Eunyoung(Regina) Kim, Hans Johnson, Mark Scully


  1. Integration of BRAINSCut into Slicer3/Slicer4
  2. Integration of GMI feature images into BRAINSCut
  3. Test BRAINSCut

Approach, Plan

  1. Check dependencies of BRAINSCut and integrate into Slicer CLM.
  2. Process test data set to verify
  3. Submit caudate results to the CAUSE07 Challenge 'http://www.cause07.org/'


  1. BRAINSCut Incorporating with Slicer3 DONE
  2. Generating BRAINSCut model for subcortical structures: caudate, putamen, thalamus, and hippocampus. DONE
  3. Verifying generated model by comparing manual traces. DONE
  4. Process 230 data to generate hippocampus. DONE


  1. Powell, S., Magnotta, V., Johnson, H., and . . . , V. J., “Registration and machine learning-based automated segmentation of subcortical and cerebellar brain . . . ,” NeuroImage (Jan 2008)
  2. Eun Young Kim, Hans Johnson, "Multi-structure segmentation of multi-modal brain images using artificial neural networks", SPIE Proceedings Paper (Mar 2010)

Download Page


Delivery Mechanism

This work will be delivered to the NAMIC Kit as a

  1. NITRIC distribution
  2. Slicer Module
    1. Built-in:
    2. Extension -- commandline:
    3. Extension -- loadable: