2010 Summer Project Week Cortical Thickness Analysis
- UNC: Clement Vachet, Heather Cody Hazlett, Martin Styner
We would like to create end-to-end applications within Slicer3 allowing voxel-based and mesh-based group analyses of 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:
Two 3D Slicer high-level modules have been developped in that regard:
- ARCTIC: Automatic Regional Cortical ThICkness
- GAMBIT: Group-wise Automatic Mesh-Based analysis of cortIcal Thickness
Our plan for the project week is to:
- Follow-up on ARCTIC: Make it directly available as a 3D Slicer extension on MAC (compilation issues apparently)
- Follow-up on GAMBIT: further developmenent
- Prodiving new 3D Slicer MRML scenes for improved quality control
- Meet with Manasi Datar and Josh Cates (Utah U.) regarding new features on ShapeWorks (future use of template/sample dataset with fixed particles...)
- ARCTIC now available as a Slicer3 extension on mac
- MRML scenes creation with snapshots for improved QC (see pics above)
- Source code development: other options...
- Particle correspondence: met with Manasi and Beatriz to include new features
- Attended QA breakout session: more tests with code coverage to be added soon on both applications!
- Attended DTI breakout session to identify steps needed to get a consistent package
This work will be delivered to the NA-MIC Kit as a:
- ITK Module
- Slicer Module
- Extension -- commandline - YES
- Extension -- loadable
- Other (Please specify)
- 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. 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 2010 abstract
- 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
- J Cates, P T Fletcher, M Styner, M Shenton, R Whitaker. Shape Modeling and Analysis with Entropy-Based Particle Systems. Information Processing in Medical Imaging IPMI 2007, LNCS 4584, pp. 333-345, 2007