Difference between revisions of "Projects/Slicer3/2007 Project Week QDEC Slicer3 Integration"

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http://www.na-mic.org/Wiki/index.php/NA-MIC/Projects/Theme/Template - Please cut and paste the template from this page and use it here. This will be the replacement for the 4-block.
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|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
 
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|[[Image:genuFAp.jpg|thumb|320px|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|thumb|320px|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.]]
 
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__NOTOC__
 
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===Key Investigators===
 
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* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig
 
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* Utah: Tom Fletcher, Ross Whitaker
 
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<h1>Objective</h1>
 
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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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<h1>Approaches and Challenges </h1>
 
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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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<h1>Progress</h1>
 
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====June 2007 Project Week====
 
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This is where you put in progress made in Project Week 2007.
 
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====January 2007 Project Half Week====
 
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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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===Publications===
 
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* Fletcher, P.T., Tao, R., Jeong, W.-K., Whitaker, R.T., "A Volumetric Approach to Quantifying Region-to-Region White Matter Connectivity in Diffusion Tensor MRI," to appear Information Processing in Medical Imaging (IPMI) 2007.
 
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* Corouge, I., Fletcher, P.T., Joshi, S., Gilmore, J.H., and Gerig, G., "Fiber Tract-Oriented Statistics for Quantitative Diffusion Tensor MRI Analysis," Medical Image Analysis 10 (2006), 786--798.
 
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* Corouge, I., Fletcher, P.T., Joshi, S., Gilmore J.H., and Gerig, G., Fiber Tract-Oriented Statistics for Quantitative Diffusion Tensor MRI Analysis, Lecture Notes in Computer Science LNCS, James S. Duncan and Guido Gerig, editors, Springer Verlag, Vol. 3749, Oct. 2005, pp. 131 -- 138
 
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* C. Goodlett, I. Corouge, M. Jomier, and G. Gerig, 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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Revision as of 02:25, 26 May 2007

Home < Projects < Slicer3 < 2007 Project Week QDEC Slicer3 Integration

http://www.na-mic.org/Wiki/index.php/NA-MIC/Projects/Theme/Template - Please cut and paste the template from this page and use it here. This will be the replacement for the 4-block.


Additional Information

Abstract

Incorporating some of the functionality of the MGH developed Freesurfer front end query tool (QDEC) into Slicer 3. Explore related issues of how to better integrate Freesurfer and Slicer3.

Discussion

  • Slicer will incorporate the basic QDEC functionality:
    • load a user-supplied table of subject data (the qdec.table.dat file)
    • display the available discrete and continous factors, and allow their selection
    • call mri_glmfit (through the C++ API, to be supplied)
    • display the overlay data
    • allow selection of a vertex, and display a scatter plot
  • What's a list of issues that need a good working solution?
    • being able to read volume encoced scalar format - done, changes made to vtkMRMLModelStorageNode
    • being able to composite scalars in Slicer3 - done, vtkMRMLModelNode::CompositeScalars (need to save the model in vtk to save the composite in mrml) FreeSurfer versus Slicer
    • picking points on models - use the fiducials interface to get at vertex ids and index into scalar overlays - done, the vtkSlicerViewerWidget class Pick method sets the picked cell ID, vertex ID - check if the Pick succeeded in finding a model node (PickedNodeName != ""), then use it to get the model node, which contains polydata that can be indexed using the vertex ID (PickedPointID)
    • FSGDF plotting
  • Identify which parts of this project are:
  1. internal developments, tightly coupled to the MGH environment
  2. features that Slicer3 might have in order to provide some qdec-type functionality to a potentially wider audience (say, BIRN users on windows)
    1. code in slicer for reading mgh file formats (mgz, surfaces, annotations, etc) into ITK and VTK which is duplicated with code used in qdec, scuba, etc.
  3. what common libraries could be shared by both of those efforts.
    1. MGH host a publicly readable svn repository, perhaps called libMGH, where all this stuff would be captured as the "official" reference implementation. MGH internal projects also rely on the library so that other users could be confident that the library is up to date and fully compatible.
  • The core QDEC engine, mri_glmfit, will be supplied as a binary, and C++ interface objects will provide the access to it, and input data loading. Slicer (and our QDEC) will compile against those C++ objects

Slide

4 block slide

Project Page

Participants

  • Nicole Aucoin BWH
  • Kevin Teich MGH
  • Nick Schmansky MGH
  • Doug Greve MGH
  • Gheorghe Postelnicu MGH
  • Steve Pieper Isomics

Back to Project week

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