Difference between revisions of "2010 Winter Project Week SegmentationWizard"

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<gallery>
 
<gallery>
 
Image:PW-SLC2010.png|[[2010_Winter_Project_Week#Projects|Projects List]]
 
Image:PW-SLC2010.png|[[2010_Winter_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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</gallery>
  
 
==Key Investigators==
 
==Key Investigators==
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* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig
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* MRN: Jeremy Bockholt, Mark Scully
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* Utah: Tom Fletcher, Ross Whitaker
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* BWN: Steve Pieper
  
 
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<h3>Objective</h3>
 
<h3>Objective</h3>
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How about finalizing the wizard for lesion segmentation using the register images module, our intensity standardization module, probabalistic bias correction, and what not.
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To implement a high level wizard that performs all necessary pre-processing steps and then segments lesion images.
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<h3>Approach, Plan</h3>
 
<h3>Approach, Plan</h3>
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'''1.''' Verify that all required sub-modules are production ready.
  
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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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'''2.''' Diagram all possible branches with requirements.
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'''3.''' Use QT to create the UI and tie all relevant modules together.
  
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Our plan for the project week is to first try out <bar>,...
 
  
 
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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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''Prior to the meeting'':
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'''1.''' Identified a number of modules to incorporate assuming they are production ready (SkullStripping, BiasCorrection, ProbabilisticBiasCorrection, RegisterImages, BrainsConstellation, etc).
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'''2.''' Implemented a number of other modules that were needed but didn't yet exist (JointIntensityStandardization, LupusLesionSegmenter)
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''At the meeting'':
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'''1.''' Met with individuals responsible for relevant modules and identified potential issues.
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'''2.''' Met with Steve Pieper on using QT for the wizard
  
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'''3.''' Worked with Hans to adapt his BRAINSABC tool to work on our data.  This accomplishes most of our preprocessing needs.
  
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'''4.''' Started implementing the wizard in QT.
 
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==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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* 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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* 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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Latest revision as of 15:45, 8 January 2010

Home < 2010 Winter Project Week SegmentationWizard

Key Investigators

  • MRN: Jeremy Bockholt, Mark Scully
  • BWN: Steve Pieper

Objective

To implement a high level wizard that performs all necessary pre-processing steps and then segments lesion images.

Approach, Plan

1. Verify that all required sub-modules are production ready.

2. Diagram all possible branches with requirements.

3. Use QT to create the UI and tie all relevant modules together.


Progress

Prior to the meeting:

1. Identified a number of modules to incorporate assuming they are production ready (SkullStripping, BiasCorrection, ProbabilisticBiasCorrection, RegisterImages, BrainsConstellation, etc).

2. Implemented a number of other modules that were needed but didn't yet exist (JointIntensityStandardization, LupusLesionSegmenter)


At the meeting:

1. Met with individuals responsible for relevant modules and identified potential issues.

2. Met with Steve Pieper on using QT for the wizard

3. Worked with Hans to adapt his BRAINSABC tool to work on our data. This accomplishes most of our preprocessing needs.

4. Started implementing the wizard in QT.

References

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