Difference between revisions of "2009 Summer Project Week Slicer3 Cortical Thickness Pipeline"
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− | Image:PW2009-v3.png|[[2009_Summer_Project_Week| | + | Image:PW2009-v3.png|[[2009_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|Brain development | Image:BrainDevelopment.jpg|Brain development | ||
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==Key Investigators== | ==Key Investigators== | ||
* UNC: Clement Vachet, Cedric Mathieu, Ipek Oguz, Marc Niethammer, Heather Cody Hazlett, Martin Styner | * UNC: Clement Vachet, Cedric Mathieu, Ipek Oguz, Marc Niethammer, Heather Cody Hazlett, Martin Styner | ||
+ | * Isomics: Steve Pieper | ||
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** Automated processing of small pediatric dataset | ** Automated processing of small pediatric dataset | ||
− | We are also interested in: | + | 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 |
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<h3>Progress</h3> | <h3>Progress</h3> | ||
+ | ARCTIC: | ||
+ | *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 | ||
+ | |||
+ | XNAT: | ||
+ | *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 | ||
</div> | </div> | ||
</div> | </div> | ||
− | <div style="width: | + | <div style="width: 97%; float: left;"> |
==References== | ==References== |
Latest revision as of 02:47, 26 June 2009
Home < 2009 Summer Project Week Slicer3 Cortical Thickness PipelineKey Investigators
- UNC: Clement Vachet, Cedric Mathieu, Ipek Oguz, Marc Niethammer, Heather Cody Hazlett, Martin Styner
- Isomics: Steve Pieper
Objective
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.
Approach, Plan
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
Progress
ARCTIC:
- 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
XNAT:
- 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
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. 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