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

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==Key Investigators==
 
==Key Investigators==
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* UNC: Yundi Shi, Martin Styner
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* UNC: Clement Vachet, Heather Cody Hazlett, Martin Styner
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* Emory: Mar Sanchez
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<div style="margin: 20px;">
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<div style="width: 27%; float: left; padding-right: 3%;">
  
 
<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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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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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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</div>
  
 
<div style="width: 27%; float: left; padding-right: 3%;">
 
<div style="width: 27%; float: left; padding-right: 3%;">
  
 
<h3>Approach, Plan</h3>
 
<h3>Approach, Plan</h3>
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** Skull stripping and Tissue segmentation
 
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ABC (developed by Marcel Prastawa, SCI, Utah) is currently used for skull stripping and tissue segmentation of the 3 months, 6 months and 12 months T1 and T2 images.
 
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Challenge include: Application of ABC or neoseg for the same task on 2 weeks old monkey images, due to the different anatomical structures during early ages and small brain size of the monkeys
 
  
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** Affine alignment
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Our approach is described in the following wiki pages:
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RVIEW is currently used for affine alignment of the monkey images. Affine registration in Slicer was tested but not producing very satisfying results.  We need to work with ?? for the special challenge in registration of the monkey brains.
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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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** Atlas building
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Two 3D Slicer high-level modules have been developped in that regard:
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Atlaswerks is the tool for atlas building with fWarp (developed by Sarang Joshi, SCI, UTAH). We would like to start using open source tools like the deamons registration in Slicer for the same task.
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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
  
 
</div>
 
</div>
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==Delivery Mechanism==
 
==Delivery Mechanism==
  
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This work will be delivered as an open-source software with open dataset.
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This work will be delivered to the NA-MIC Kit as a:
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#ITK Module
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#Slicer Module
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##Built-in
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##Extension -- commandline - YES
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##Extension -- loadable
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#Other (Please specify)
  
 
==References==
 
==References==
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** M. Styner, R. Knickmeyer, S. Joshi, C. Coe, S. J. Short, and J. Gilmore. Automatic brain segmentation in rhesus monkeys. In Proc SPIE Vol 6512, Medical Imaging, 2007, pp. 65122 L1-8..
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*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.
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*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.
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*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
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*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
  
 
</div>
 
</div>

Revision as of 20:54, 16 June 2010

Home < 2010 Summer Project Week Cortical Thickness Analysis


Key Investigators

  • UNC: Clement Vachet, Heather Cody Hazlett, Martin Styner

Objective

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.




Approach, Plan

Our approach is described in the following wiki pages:

Two 3D Slicer high-level modules have been developped in that regard:

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, e.g by prodiving new 3D Slicer MRML scenes for quality control

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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