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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 #==
1R01NS050568

==Key Personnel==
The collaborators include Vincent Magnotta, Hans Johnson, Jeremy Bockholt, and Nancy Andreasen. 

==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]]

=== Code Refactoring for Cross Platform Support ===
*[[Refactor Current Modules using ITK and VTK]]
*[[Build GUI using Slicer3 Interface]]
*[[Use Python as Scripting Language]]

=== Validation of Pipeline Using MIND MCIC Sample ===
*[[Evaluate MIND MCIC Human Phantom Sample Using Automated Pipeline]] 
*[[Evaluate Differences between Patients with Schizophrenia and Normal Controls using Automated 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. [http://www.nitrc.org/projects/multimodereg/ BRAINSFit NITRC Link]
*[http://www.nitrc.org/projects/brainsdemonwarp/ BRAINSDemonsWarp] - Non-linear registration of two image sets. This includes the diffeomorphic demons algorithm along with a number of useful enhancements. 
*[http://www.nitrc.org/projects/brainsmush/ BRAINSMush] - Tool to combine T1 and T2 datasets into a composite image. The resulting image is then used to perform brain extraction.
*[http://www.nitrc.org/projects/brainscut/ BRAINSCut] - Automated segmentation of subcortical and cerebellar regions of interest using an artificial neural network.
*[http://www.nitrc.org/projects/brainstracer/ BRAINSTracer] - Tracing tool that uses thge vtkContourWidget for defining a region of interest manually
*[http://www.nitrc.org/projects/vmagnotta/ GTRACT] - Diffusion tensor analysis and Fiber tracking tool
*[http://www.nitrc.org/projects/brains/ BRAINS Auto Workup] - Fully automated image analysis pipeline for generation of volumetric measurements.

=== BRAINS Features ===
<gallery caption="BRAINS Gallery" widths="200px" heights="200px" perrow="3">
Image:Surface-Depth.gif|BRAINS Surface showing cortical depth
Image:Surface-Curvature.gif|BRAINS Surface showing curvature (ie sulcal and gyral labels)
Image:BRAINS-Tissue-Clasification.gif|BRAINS Continuous Tissue Classification
Image:ANN-Axial.gif|Automated segmentation of Subcortical nuclei using Neural Networks
Image:BRAINS-Image-Registration.gif|BRAINS Image Registration using ITK Mutual Information
Image:FLAIR-Lesion-Labels.gif|Lesion identification with FLAIR, T1 and T2 weighted images
Image:BRAINS-Talairach-Labels.gif|Talairach lobar labels
Image:GTRACT-Fiber-Tracking.gif|GTRACT DTI fiber tracking
</gallery>

==Publications==
# Powell S, Magnotta VA, Johnson H, Jammalamadaka VK, Pierson R, Andreasen NC. Registration and machine learning-based automated segmentation of subcortical and cerebellar brain structures.  Neuroimage. 2007 Aug 22; [Epub ahead of print].

==Meetings==
==Resource Links==