CCB Software and Tool-Development Projects

Summary

This page describes a variety of CCB computational Projects that need design, implementation, testing, Grid-porting, packaging and dissemination of novel CCB algorithms, methods and research/prototype code. These projects may involve writing new code, redesign of existent software, conversion from one language to another, building/packaging or tools, improving tool interfaces (graphical or command-driven), etc. Many of the CCB novel tools are also briefly described here.

Project 1: Hippocampal surface mapping tool

• Project Description: This tool will compute the mapping of hippocampal surfaces from different input formats.
• Computational Neuroscience Problem addressed by this Research Project: Statistical shape analysis of HC surfaces from disease groups and normal controls.
• Research Project Leader(s): Yonggang Shi
• SW Project Leader and Members:
• Project Specific Needs: Integrating existing codes of different modules into a user friendly software. Automatic script generation for group studies on Grid.
• Estimated development timeline, milestones and deliverables: 3 ~ 6 months.
• Project Specs Page

Project 2: Direct cortical mapping tool

• Project Description: This tool will compute the mapping of cortical surfaces with landmark constraints.
• Computational Neuroscience Problem addressed by this Research Project: Establish correspondence between points on cortical surfaces for further statistical testing.
• Research Project Leader(s): Yonggang Shi
• SW Project Leader and Members:
• Project Specific Needs: Integrating existing codes of different modules into a user friendly software. Automatic script generation for group studies on Grid.
• Estimated development timeline, milestones and deliverables: 2 months.

Project 3: Brain sub-cortical structure parsing

• Project Description: This tool will segment an MRI volume into various sub-cortical structures
• Computational Neuroscience Problem addressed by this Research Project: Multi-class classification training/testing, learning shape statistics
• Research Project Leader(s): Zhuowen Tu
• SW Project Leader and Members:
• Project Specific Needs: transferring existing codes written in Visual .Net into Linux/unix
• Estimated development timeline, milestones and deliverables: 2 months.

Project 4: Major sulci detection

• Project Description: This tool will automatically detect major sulci
• Computational Neuroscience Problem addressed by this Research Project: Twi-class classification training/testing, learning shape statistics
• Research Project Leader(s): Zhuowen Tu
• SW Project Leader and Members: Songfeng Zhen
• Project Specific Needs: transferring existing codes written in Visual .Net into Linux/unix
• Estimated development timeline, milestones and deliverables: 2 months.

Project 5: Distributed image registration using grid computing

• Project Description: We explore the space of input parameters of different image registration tools (2D and 3D), run the tools with those parameters, and propose solutions from the results obtained according to some comparison metrics we implemented.
• Computational Neuroscience Problem addressed by this Research Project: Image registration
• Research Project Leader(s): Alex Cunha
• SW Project Leader and Members: Alex (leader)
• Project Specific Needs: Willingness to understand image registration as a practical problem and work with different image registration tools and APIs. Your work will be part of a larger system that integrates diverse image registrattion tools. Programming in any language of your preference (C++, C, Java, Perl, Python - we will install the compiler you need to work with) for Solaris and Linux OS. Create filters for specific data formats. Collect and prepare data sets (image files). CCB_Tools_MeiheXu_SurfaceExtractionTutorialUsage of the Pipeline engine.
• Estimated development timeline, milestones and deliverables: First stage : experiment with image registration tools and write code to create displacement field filters for them; Second stage : Collect and prepare data sets for studies; Third Stage : Create Pipeline modules for our codes and generate results using our Grid computer. 1 to 3 months.
• Project Specs Page

Project 6: CCB/NCBC prototype framework for dynamic graphical management of the NCBC Resources.

• Project Specs Page

Project 7: Level-Sets based Methods for analyzing fMRI Data.

• Project Specs Page

Project 8: Tissue Segmentation/Classification using Level-Set-based Methods.

• Project Specs Page

Project 9: Yalin/Boris Shape Tools.

• Project Specs Page

Project 10: Shape-Atlas Project.

• Project Specs Page