Difference between revisions of "2010 Summer Project Week Cortical Thickness Analysis"

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==Key Investigators==
 
==Key Investigators==
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* UNC: Clement Vachet, Heather Cody Hazlett, Martin Styner
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* UNC: Yundi Shi, Martin Styner
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* Emory: Mar Sanchez
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<h3>Objective</h3>
 
<h3>Objective</h3>
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We would like to create end-to-end applications within Slicer3 allowing voxel-based and mesh-based group analyses of cortical thickness.  
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To build an open-source software (mainly involving Slicer3) based pipeline for primate imaging, including skull stripping of T1,T2 and DTI images, tissue segmentation, cortical thickness analysis, atlas building and fiber tracing and tract-based analysis. This is part of a longitudinal study of rhesus macaque monkeys
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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 [[DBP2:UNC|autism (UNC DBP)]].
 
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See our [[DBP2:UNC:Cortical_Thickness_Roadmap| Roadmap]] for more details.
 
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<h3>Approach, Plan</h3>
 
<h3>Approach, Plan</h3>
  
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Our approach is described in the following wiki pages:
 
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*[[DBP2:UNC:Regional_Cortical_Thickness_Pipeline|Voxel-based regional cortical thickness analysis]]
 
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*[[DBP2:UNC:Local_Cortical_Thickness_Pipeline|Mesh-based local cortical thickness analysis]]
 
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Two 3D Slicer high-level modules have been developped in that regard:
 
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*[http://www.nitrc.org/projects/arctic ARCTIC: Automatic Regional Cortical ThICkness]
 
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*[http://www.nitrc.org/projects/gambit GAMBIT: Group-wise Automatic Mesh-Based analysis of cortIcal Thickness ]
 
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Our plan for the project week is to:
 
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* Follow-up on ARCTIC: Make it directly available as a 3D Slicer extension on MAC (compilation issues apparently)
 
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* Follow-up on GAMBIT: further developmenent, e.g by prodiving new 3D Slicer MRML scenes for quality control
 
  
 
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Revision as of 20:38, 16 June 2010

Home < 2010 Summer Project Week Cortical Thickness Analysis


Key Investigators

  • UNC: Yundi Shi, Martin Styner
  • Emory: Mar Sanchez

Objective

To build an open-source software (mainly involving Slicer3) based pipeline for primate imaging, including skull stripping of T1,T2 and DTI images, tissue segmentation, cortical thickness analysis, atlas building and fiber tracing and tract-based analysis. This is part of a longitudinal study of rhesus macaque monkeys

Approach, Plan


Progress


Delivery Mechanism

This work will be delivered to the NA-MIC Kit as a:

  1. ITK Module
  2. Slicer Module
    1. Built-in
    2. Extension -- commandline - YES
    3. Extension -- loadable
  3. Other (Please specify)

References

  • 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
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