2009 Summer Project Week Slicer3 Cortical Thickness Pipeline
- UNC: Clement Vachet, Cedric Mathieu, Ipek Oguz, Marc Niethammer, Heather Cody Hazlett, Martin Styner
- Isomics: Steve Pieper
We would like to create end-to-end applications within Slicer3 allowing individual and group analysis of regional (voxel-based) and local (mesh-based) cortical thickness.
Such a workflow applied to the young brain (2-4 years old) is our goal in order to start a longitudinal study of early brain development in autism (UNC DBP).
See our Roadmap for more details.
Our approach is described in the following wiki pages:
Our plan for the project week is to:
- Improve ARCTIC's integration within Slicer3
- Continue on the mesh-based cortical thickness pipeline.
- Particle correspondence individual testing
- Automated processing of small pediatric dataset
We are also interested in learning about:
- batch-processing within Slicer3 to perform group analysis
- XNAT integration to be able to download atlases within Slicer3 needed by our pipelines
- Interaction with ARCTIC user (Jorge Alvarado) -> bug fixed
- ARCTIC 1.2: new release and new tutorial available on NITRC
- Learnt about Slicer3 extension model: ARCTIC available with this method
- Attended the beakout cession
- Met with Wendy and Beatriz regarding XNAT and the use of FetchMi for future improvement
Mesh-based cortical thickness pipeline:
- Small dataset currently being processed
- I. Oguz, M. Niethammer, J. Cates, R. Whitaker, T. Fletcher, C. Vachet, and M. Styner, Cortical Correspondence with Probabilistic Fiber Connectivity, Information Processing in Medical Imaging, IPMI 2009, LNCS, in print.
- H.C. Hazlett, C. Vachet, C. Mathieu, M. Styner, J. Piven, Use of the Slicer3 Toolkit to Produce Regional Cortical Thickness Measurement of Pediatric MRI Data, presented at the 8th Annual International Meeting for Autism Research (IMFAR) Chicago, IL 2009.
- C. Mathieu, C. Vachet, H.C. Hazlett, G. Geric, J. Piven, and M. Styner, ARCTIC – Automatic Regional Cortical ThICkness Tool, UNC Radiology Research Day 2009 abstract
- C. Vachet, H.C. Hazlett, M. Niethammer, I. Oguz, J.Cates, R. Whitaker, J. Piven, M. Styner, Mesh-based Local Cortical Thickness Framework, UNC Radiology Research Day 2009 abstract