NA-MIC Brains Collaboration

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This project is not an NCBC collaboration grant, but instead a Continued Development and Maintenance of Software grant. The intent of this application is to update the BRAINS image analysis software developed at the University of Iowa.



Key Personnel

  • University of Iowa: Vincent Magnotta, PI, Hans Johnson, Jeremy Bockholt, and Nancy Andreasen
  • NA-MIC: Steve Pieper (Isomics)

Funding Duration



There are three main thrusts of this application as outlined below.

Implement an Automated Brain Analysis Pipeline

Validation of Pipeline

Tools Developed

Here is a list of tools that are being developed as part of this project. A number of these tools have been contributed to the NITRC website. All of the tools are built upon the Slicer3 execution model and therefore will readily plug-in to Slicer3.

  • BRAINSFit - Linear fitting of two 3D image sets using a mutual information similarity metric. NITRC Link
  • BRAINSDemonsWarp - Non-linear registration of two image sets. This includes the diffeomorphic demons algorithm along with a number of useful enhancements. NITRC Link
  • BRAINSMush - Tool to combine T1 and T2 datasets into a composite image. The resulting image is then used to perform brain extraction. NITRC Link
  • BRAINSCut - Automated segmentation of subcortical and cerebellar regions of interest using an artificial neural network. NITRC Link
  • BRAINSTracer - Tracing tool that uses thge vtkContourWidget for defining a region of interest manually. NITRC Link
  • GTRACT - Diffusion tensor analysis and Fiber tracking tool. NITRC Link
  • BRAINS Automated Pipeline - Fully automated image analysis pipeline for generation of volumetric measurements. NITRC Link

BRAINS Features



Resource Links