Structural and Functional Imaging
Co-Chairs
David Van Essen and Ragini Verma
Working Group Participants
- David van Essen
- Balaji Gandhi
- Steve Koslow
- Isaac Trotts
- Volker Hartenstein
- Jack van Horn
- Ed Bullmore
- Andrew Poliakov
- Glenn Rosen
- Joseph Maldjian
- Jeffrey Gratha
- Susumu Mori
- Christian Haselgrove
- David Kennedy
- Jinmin Zhu
- Bitao Shi
- Gail Hamilton
- Adrian Robert
- Zhong Xue
- Ragini Verma
- Reza [Need full name]
Meeting outcome
- Combine subcommittees
- Image analysis tools description & evaluation
- Pipeline and terminology
- Two directions to be followed:
- fMRI pipeline development
- Development & collection of evaluation datasets
- Possible third direction: development of evaluation tools
fMRI pipeline development
- To be led by: Dave Kennedy + Ed Bullmore
- Identify groups/software dealing with fMRI processing on IATR
- Contact groups to:
- Modularize software (starting with niFTi compatible tools)
- Enable the processing pipeline to become "plug & play" — interoperability of tool components
- Proof concept on fMRI pipeline: can then be extended to other pipelines + structural imaging tools
Evaluation datasets
- Efforts led by: Jack van Horn + Ragini Verma
- Create website/WIKI site with the following:
- Evaluation dataset
- Types of dataset
- Information about each dataset
- What it has been used to evaluate to date
- Brain Atlases
- Contact members of the group as well as the community outside (IATR contributers?); determine which datasets they use for evaluation / brain atlases
- IATR: With each tool, list dataset evaluate on, provide peer-reviewed publication
Evaluation datasets
- Types of dataset
- Simulated datasets [SBIA (atrophy + growth), fMRI simulation (BPM — Wake Forest)]
- Evaluation of Acquisition protocols (BIRN traveling phantom)
- Real datasets [fMRI + DTI (Susumu Mori)] — peer reviewed
- Human labeled data
- Information about each dataset
- Scanner info
- Format (recommend nifTi compatibility)
- Cognitive paradigm
- fMRI: stimuli administered, details …
- What evaluation for which the dataset is best suited
- fMRI dataset should have supporting structural
- DTI datasets
- Identify anonymization tool used or the need for one
Brain atlases
- List existing atlases (templates + ROI definitions)
- MNI atlas
- PICKatlas (Wake Forest)
- CARET
- Jacob brain
- White matter atlas — DTI (Susumu Mori)
- Methods of linking atlases (registration)
Evaluation tools
- Identified as a possible third outcome
- Define metrics & comparative evaluation
- Working group suggested that Steve Strother be requested to follow up on this
- Could be added to the "Evaluation datasets" website
Immediate next steps
- Updating all members of the working group with the plans proposed / discussed in the meeting
- Setting up of the "Evaluation dataset + Brain Atlases" website
- Soliciting contributions
- Identifying the fMRI community on IATR to begin modularizing the software
- Encourage LM/EM/Histology members to continue developing pipeline and updating the group
- Contact Steve Strother about "Evaluation Tools"
