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.
- University of Iowa: Vincent Magnotta, PI, Hans Johnson, Jeremy Bockholt, and Nancy Andreasen
- NA-MIC: Steve Pieper (Isomics)
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
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
- Powell S., Magnotta V.A., Johnson H., Jammalamadaka V.K., Pierson R., Andreasen N.C. 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.