NA-MIC Brains Collaboration

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Abstract

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.

Grant#

R01NS050568

Key Personnel

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

Funding Duration

05/15/2007-03/31/2010

Projects

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

Implement an Automated Brain Analysis Pipeline

• BRAINS Automated Pipeline
• Support for Batch Processing
• Visual Review and Verification of Results
• Build GUI using Slicer3 Interface

Validation of Pipeline

• Evaluate MIND MCIC Human Phantom Sample Using Automated Pipeline
• Evaluate of DTI Reliability Across Sites and Platforms

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

• BRAINS Gallery
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  BRAINS Surface showing cortical depth

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  BRAINS Surface showing curvature (ie sulcal and gyral labels)

• 

  BRAINS Continuous Tissue Classification

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  Automated segmentation of Subcortical nuclei using Neural Networks

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  BRAINS Image Registration using ITK Mutual Information

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  Lesion identification with FLAIR, T1 and T2 weighted images

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  Talairach lobar labels

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  GTRACT DTI fiber tracking

Publications

• Powell S, Magnotta V, Johnson H, Jammalamadaka V, Pierson R, Andreasen N. Registration and machine learning-based automated segmentation of subcortical and cerebellar brain structures. Neuroimage. 2008 Jan 1;39(1):238-47. PMID: 17904870. PMCID: PMC2253948.