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

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Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
 
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
 
Image:Arctic_Logo.png‎|[http://www.nitrc.org/projects/arctic ARCTIC: Automatic Regional Cortical ThICkness]
 
Image:Arctic_Logo.png‎|[http://www.nitrc.org/projects/arctic ARCTIC: Automatic Regional Cortical ThICkness]
−
Image:BrainDevelopment.jpg|[http://www.nitrc.org/projects/gambit GAMBIT: Group-wise Automatic Mesh-Based analysis of cortIcal Thickness ]
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Image:GAMBITLogo.png|[http://www.nitrc.org/projects/gambit GAMBIT: Group-wise Automatic Mesh-Based analysis of cortIcal Thickness]
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Image:MeshBasedCortThick_CorticalThickness.jpg|Cortical thickness on white matter surface
 
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Image:MeshBasedCortThick_SulcalDepth.jpg‎|Sucal depth on genus-zero cortical surface
 
 
Image:MeshBasedCortThick_Particles.jpg‎|Particles on inflated genus-zero cortical surface
 
Image:MeshBasedCortThick_Particles.jpg‎|Particles on inflated genus-zero cortical surface
 
</gallery>
 
</gallery>
 +
{|
 +
| [[Image:GAMBIT_QC_CorticalThickness.png|thumb|500px|Cortical thickness overlayed on inflated cortical surfaces]]
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| [[Image:GAMBIT_QC_SulcalDepth.png|thumb|500px|Sulcal depth overlayed on inflated cortical surfaces]]
 +
|}
  
 +
==Key Investigators==
 +
* UNC: Clement Vachet, Heather Cody Hazlett, Martin Styner
  
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==Key Investigators==
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<div style="margin: 20px;">
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* UNC: Yundi Shi, Martin Styner
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<div style="width: 27%; float: left; padding-right: 3%;">
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* Emory: Mar Sanchez
 
  
 
<h3>Objective</h3>
 
<h3>Objective</h3>
−
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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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 [[DBP2:UNC|autism (UNC DBP)]].
 +
 +
See our [[DBP2:UNC:Cortical_Thickness_Roadmap| Roadmap]] for more details.
 +
 +
 +
 +
 +
 +
 +
</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>
−
** Skull stripping and Tissue segmentation
 
−
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.
 
−
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
 
  
−
** Affine alignment
+
Our approach is described in the following wiki pages:
−
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.
+
*[[DBP2:UNC:Regional_Cortical_Thickness_Pipeline|Voxel-based regional cortical thickness analysis]]
 +
*[[DBP2:UNC:Local_Cortical_Thickness_Pipeline|Mesh-based local cortical thickness analysis]]
  
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** Atlas building
+
Two 3D Slicer high-level modules have been developped in that regard:
−
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.
+
*[http://www.nitrc.org/projects/arctic ARCTIC: Automatic Regional Cortical ThICkness]
 +
*[http://www.nitrc.org/projects/gambit 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...)
  
 
</div>
 
</div>
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<h3>Progress</h3>
 
<h3>Progress</h3>
 +
* ARCTIC now available as a Slicer3 extension on mac
 +
* GAMBIT:
 +
** 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
  
  
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==Delivery Mechanism==
 
==Delivery Mechanism==
  
−
This work will be delivered as an open-source software with open dataset.
+
This work will be delivered to the NA-MIC Kit as a:
 +
 
 +
#ITK Module
 +
#Slicer Module
 +
##Built-in
 +
##Extension -- commandline - YES
 +
##Extension -- loadable
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#Other (Please specify)
  
 
==References==
 
==References==
−
** 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.
 +
*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
  
 
</div>
 
</div>

Latest revision as of 20:42, 13 December 2010

Home < 2010 Summer Project Week Cortical Thickness Analysis
Cortical thickness overlayed on inflated cortical surfaces
Sulcal depth overlayed on inflated cortical surfaces

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
    • 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...)

Progress

  • ARCTIC now available as a Slicer3 extension on mac
  • GAMBIT:
    • 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


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
  • 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
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