Difference between revisions of "2012 Summer Project Week:QuantitativePETImageAnalysisModule"

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Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
 
Image:PW-MIT2012.png|[[2012_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:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.
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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 2012_Winter_Project_Week:<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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* University of Iowa: Christian Bauer, Reinhard Beichel, Markus Van Tol, ...?
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* Utah: Tom Fletcher, Ross Whitaker
 
  
 
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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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We are developing a loadable module for Slicer to allow for threshold-based segmentation of tumors (or other regions of uptake) in PET scans within user-specified bounds and the tracking of such tumors. This would be used so that multiple physicians could segment the tumor and all consistently create one segmentation.  With this, further work would go into checking values such as size and intensity values of tumors, which could be compared over time.
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This project may become a part of another: [http://www.na-mic.org/Wiki/index.php/2012_Summer_Project_Week:LongitudinalPETCTModule http://www.na-mic.org/Wiki/index.php/2012_Summer_Project_Week:LongitudinalPETCTModule]
  
 
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<h3>Approach, Plan</h3>
 
<h3>Approach, Plan</h3>
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Tasks, in order of importance/doability at this project week:
  
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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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1. Set up module testing so it can expand as the rest of the module expands.
  
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Our plan for the project week is to first try out <bar>,...
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2. Start on the section for comparing segmentations in different images over time. (Would need information on relating data sets over time)
  
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3. Debug issues with saving the scene and interacting with the Annotations module.
 
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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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Before project week:
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Created a loadable module that currently allows threshold-based segmentation in user-defined regions of interest. Currently designed for PET scan images. Has functionality to suggest a threshold in a space and exclude other regions by uptake values or by user-defined excluded regions and points.
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Fully functional without the need to change to another module.
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After project week:
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Didn't end up working on things in approach.  Instead, worked on creating a spherical region of interest (SROI) for annotations.  This is currently partially done and reasonably functional, if not as apparent as desired.
  
 
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##Built-in
 
##Built-in
 
##Extension -- commandline
 
##Extension -- commandline
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##Extension -- loadable
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##Extension -- loadable YES
 
#Other (Please specify)
 
#Other (Please specify)
  
 
==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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* Reinhard Beichel's UIowa staff page: [http://www.engineering.uiowa.edu/~rbeichel/index.html http://www.engineering.uiowa.edu/~rbeichel/index.html]
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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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* Quantitative Imaging Network (QIN) page: [http://imaging.cancer.gov/programsandresources/specializedinitiatives/qin http://imaging.cancer.gov/programsandresources/specializedinitiatives/qin]
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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 .
 
  
 
</div>
 
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Latest revision as of 12:34, 22 June 2012

Home < 2012 Summer Project Week:QuantitativePETImageAnalysisModule

  • Incomplete Sphere, starting to scale

  • Incomplete Sphere, after scaling


Key Investigators

  • University of Iowa: Christian Bauer, Reinhard Beichel, Markus Van Tol, ...?

Objective

We are developing a loadable module for Slicer to allow for threshold-based segmentation of tumors (or other regions of uptake) in PET scans within user-specified bounds and the tracking of such tumors. This would be used so that multiple physicians could segment the tumor and all consistently create one segmentation. With this, further work would go into checking values such as size and intensity values of tumors, which could be compared over time.

This project may become a part of another: http://www.na-mic.org/Wiki/index.php/2012_Summer_Project_Week:LongitudinalPETCTModule

Approach, Plan

Tasks, in order of importance/doability at this project week:

1. Set up module testing so it can expand as the rest of the module expands.

2. Start on the section for comparing segmentations in different images over time. (Would need information on relating data sets over time)

3. Debug issues with saving the scene and interacting with the Annotations module.

Progress

Before project week: Created a loadable module that currently allows threshold-based segmentation in user-defined regions of interest. Currently designed for PET scan images. Has functionality to suggest a threshold in a space and exclude other regions by uptake values or by user-defined excluded regions and points. Fully functional without the need to change to another module.


After project week: Didn't end up working on things in approach. Instead, worked on creating a spherical region of interest (SROI) for annotations. This is currently partially done and reasonably functional, if not as apparent as desired.

Delivery Mechanism

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

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

References

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