Collaboration/Iowa/Meshing/Migrate Iowa Neural Net code to pure ITK

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Home < Collaboration < Iowa < Meshing < Migrate Iowa Neural Net code to pure ITK
Atlas Hand Image
Subject Hand Image
Warped Atlas Image

Key Investigators

  • Iowa: Vincent Magnotta and Nicole Grosland
  • Kitware: Stephen Alyward


Conversion of the Iowa Neural netwok segmentation using a flexible module for image registration supporting all ITK transforms written using the transform I/O in ITK. Conversion to the ITK neural network from the current annie implementation may also be

Approach, Plan

Integrate additional ITK transform types into the neural network using the general ITK transform I/O mechanism. Evaluate the changes to segment the phalanx bones bones of the hand.


Two milestones were reached in this effort.

  • The first was that we have integrated a rigid body initialization for a Thirion Demons registration for atlas <-> subject registration. The above modification was used to warp the atlas to the subject as shown in the figures.
  • The second was that the neural network code now supports all ITK transforms for registration of the atlas<->subject. This was achieved using the itkTransformReader and the a templated function over the image type and transform type to resample the images.


  • Magnotta VA, Heckel D, Andreasen NC, Cizadlo T, Corson PW, Ehrhardt JC, Yuh WT. "Measurement of brain structures with artificial neural networks: two- and three-dimensional applications", Radiology 211 (1999), 781-90.
  • Powell S, Magnotta VA, Johnson HJ, Jammalamadaka VK, Andreasen NC. "Registration and Machine Learning Based Automated Segmentation of Subcortical and Cerebellar Brain Structures", NeuroImage, In Press.