Difference between revisions of "2009 Summer Project Week Liver Ablation Slicer"

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(Created page with '__NOTOC__ <gallery> Image:PW2009-v3.png|Project Week Main Page Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus ...')
 
 
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__NOTOC__
 
__NOTOC__
 
<gallery>
 
<gallery>
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Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
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Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Projects List]]
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Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.
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Image:originalSegmentation.png|Segmentation showing no pass zones (ribs)and tumor.
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Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.
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Image:segmentationAfterDilation.png|Segmented tumor region is dilated according to physician prescribed ablation margin.
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Image:Slicer_liver_module.png|IGT planning module for liver albation in Slicer3.
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Image:Segmentation_dilated_by_slicer.png|Segmented tumor region is dilated in Slicer3.
 
</gallery>
 
</gallery>
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==Instructions for Use of this Template==
 
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#Please create a new wiki page with an appropriate title for your project using the convention Project/<Project Name>
 
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#Copy the entire text of this page into the page created above
 
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#Link the created page into the list of projects for the project event
 
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#Delete this section from the created page
 
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#Send an email to tkapur at bwh.harvard.edu if you are stuck
 
  
 
==Key Investigators==
 
==Key Investigators==
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* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig
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* BWH: Haiying Liu, Noby Hata
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* Utah: Tom Fletcher, Ross Whitaker
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* Georgetown: Ziv Yaniv
  
 
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<h3>Objective</h3>
 
<h3>Objective</h3>
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We are developing methods for analyzing diffusion tensor data along fiber tracts. The goal is to be able to make statistical group comparisons with fiber tracts as a common reference frame for comparison.
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Implement a complete workflow:
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#Load data.
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#Manually mark regions (tumor, entry, critical structure).
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#Process segmentation and export information to planning module (executable plugin with command line options).
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#Load results of the optimization program.
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#Configure OpenIGTLink module on Slicer and run OpenIGTLink IGSTK client.  
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#Navigate.
 
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<h3>Approach, Plan</h3>
 
<h3>Approach, Plan</h3>
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Our approach for analyzing diffusion tensors is summarized in the IPMI 2007 reference below.  The main challenge to this approach is <foo>.
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#Integrate code from Georgetown for step 3 into Slicer.
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#Decide on appropriate format for describing the output of the optimization (set of trajectories and ablations along each trajectory).
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Our plan for the project week is to first try out <bar>,...
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#Implement a stub executable plugin as a stand in for the optimization program.
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#Test the integrated workflow.
 
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<h3>Progress</h3>
 
<h3>Progress</h3>
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Software for the fiber tracking and statistical analysis along the tracts has been implemented. The statistical methods for diffusion tensors are implemented as ITK code as part of the [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|DTI Software Infrastructure]] project. The methods have been validated on a repeated scan of a healthy individual. This work has been published as a conference paper (MICCAI 2005) and a journal version (MEDIA 2006). Our recent IPMI 2007 paper includes a nonparametric regression method for analyzing data along a fiber tract.
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* Completed GUI design and implementation for "planning" part of the workflow.
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* An unique feature in the planning part were tumor segmentation and ablation volume planning, taking ablation magin into account.
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* "Navigation" part 80% done.
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* In "Navigation", "IGT Guidance" widget was designed and implemented to be shared with other IGT investigators.
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</div>
 
</div>
 
</div>
 
</div>
  
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<div style="width: 97%; float: left;">
  
 
==References==
 
==References==
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*Fletcher P, Tao R, Jeong W, Whitaker R. [http://www.na-mic.org/publications/item/view/634 A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI.] Inf Process Med Imaging. 2007;20:346-358. PMID: 17633712.
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*Z. Yaniv, E. Wilson, D. Lindisch, K. Cleary, "Electromagnetic Tracking in the Clinical Environment", Med. Phys., Vol. 36(3), pp. 876-892, 2009. PMID: 19378748
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* Corouge I, Fletcher P, Joshi S, Gouttard S, Gerig G. [http://www.na-mic.org/publications/item/view/292 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Med Image Anal. 2006 Oct;10(5):786-98. PMID: 16926104.
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*J. Tokuda et al., "OpenIGTLink: An open network protocol for image- guided therapy environment," International Journal of Medical Robotics and Computer Assisted Surgery, to appear.
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* Corouge I, Fletcher P, Joshi S, Gilmore J, Gerig G. [http://www.na-mic.org/publications/item/view/1122 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Int Conf Med Image Comput Comput Assist Interv. 2005;8(Pt 1):131-9. PMID: 16685838.
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* Goodlett C, Corouge I, Jomier M, Gerig G, A Quantitative DTI Fiber Tract Analysis Suite, The Insight Journal, vol. ISC/NAMIC/ MICCAI Workshop on Open-Source Software, 2005, Online publication: http://hdl.handle.net/1926/39 .
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</div>

Latest revision as of 15:16, 26 June 2009

Home < 2009 Summer Project Week Liver Ablation Slicer

  • Segmentation showing no pass zones (ribs)and tumor.

  • Segmented tumor region is dilated according to physician prescribed ablation margin.

  • IGT planning module for liver albation in Slicer3.

  • Segmented tumor region is dilated in Slicer3.

Key Investigators

  • BWH: Haiying Liu, Noby Hata
  • Georgetown: Ziv Yaniv

Objective

Implement a complete workflow:

  1. Load data.
  2. Manually mark regions (tumor, entry, critical structure).
  3. Process segmentation and export information to planning module (executable plugin with command line options).
  4. Load results of the optimization program.
  5. Configure OpenIGTLink module on Slicer and run OpenIGTLink IGSTK client.
  6. Navigate.

Approach, Plan

  1. Integrate code from Georgetown for step 3 into Slicer.
  2. Decide on appropriate format for describing the output of the optimization (set of trajectories and ablations along each trajectory).
  3. Implement a stub executable plugin as a stand in for the optimization program.
  4. Test the integrated workflow.

Progress

  • Completed GUI design and implementation for "planning" part of the workflow.
  • An unique feature in the planning part were tumor segmentation and ablation volume planning, taking ablation magin into account.
  • "Navigation" part 80% done.
  • In "Navigation", "IGT Guidance" widget was designed and implemented to be shared with other IGT investigators.


References

  • Z. Yaniv, E. Wilson, D. Lindisch, K. Cleary, "Electromagnetic Tracking in the Clinical Environment", Med. Phys., Vol. 36(3), pp. 876-892, 2009. PMID: 19378748
  • J. Tokuda et al., "OpenIGTLink: An open network protocol for image- guided therapy environment," International Journal of Medical Robotics and Computer Assisted Surgery, to appear.
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