View source for 2009 Summer Project Week Hageman FMTractography

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|[[Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:Hageman_cspfig4NAMIC_07-06-22.png|thumb|320px|Corticospinal tracts segmented using our fluid mechanics based tractography method.]]
|[[Image:Hageman_FullBrainSlicerTractography.jpg|thumb|320px|Full brain tracts segmented using multiple fluid sources/sinks.]]
|[[Image:FMModuleScreenshot.png|thumb|320px|Screenshot of Slicer Module for Fluid Mechanics Tractography.]]
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===Key Investigators===
* UCLA: Nathan Hageman
* UCLA: Arthur Toga, Ph.D
* Isomics: Steve Pieper and Alex Yarmarkovich


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<h1>Objective</h1>
Computational fluid dynamics is a rich field and its application to the analysis of diffusion tensor imaging (DTI) datasets has yielded possible applications to tractography, image registration, and white matter pathology.  We are developing several useful and novel diffusion tensor imaging (DTI) analysis algorithms modeled on the principles of fluid mechanics for inclusion within the NA-MIC framework.  The goal of this project is to develop these methods, make them compatible with the NA-MIC ITK-based software infrastructure (i.e. Slicer), and promote their dissemination to the scientific community.

See our [[hageman:NAMICFluidMechDTITractography|Project Page]] for more information.

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<h1>Approach, Plan</h1>

We have developed and initially validated a DTI tractography method based on Navier-Stokes fluid mechanics.  See the papers listed in the reference section for complete details on the method.  Our approach for this project week will focus on the following: 
* Building the our current CL Slicer module into an interactive GUI in Slicer 3.  Our method is currently integrated as a CL Slicer module in a custom build of Slicer 3.  The module has the following functionalities:
**reconstruction of the diffusion tensor and computation of common DTI scalar volumes (FA, LI, RGB).  In addition, if users prefer using their own tensor reconstruction methods, the module can be run with any arbitrary set of tensor volumes.
**computation of fluid velocity vector field volume
**reconstruction of tracts based on the above fluid velocity volume
** Optimizing initial coding of method in ITK (better use of multithreading)
** Specialized visualization using VTK:
*** Fluid velocity vector field animation
*** Layout for Slicer 3 Plug-in
*** Interactive (real-time) manipulation of sources/sinks (ROIs) on steady-state fluid solution (possible application for intra-operative DTI)
* Working with the interested groups in analyzing control and white matter pathology data.  Specifically, we have seen promising results when looking at the flow perturbation around white matter lesions seen in multiple sclerosis or stroke that may suggest a novel method for automatic lesion detection in DTI.  
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<h1>Progress</h1>
* Command line fluid mechanics tractography module integrated into Slicer 3 (see snapshot above)
* VTK module for fluid mechanics visualization completed.
** Discussion of possibly including module in next stable Slicer release.
** Progress made on (near) real time fluid velocity vector field animation but not yet stable for release.
* Arrangements made to include FM tractography method as part of DTI validation effort. 
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===References===
* Hageman NS, Shattuck DW, Narr K, Toga AW (2006).  A diffusion tensor imaging tractography method based on Navier-Stokes fluid mechanics. Proceedings of the 2006 IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2006), Arlington, VA, USA, 6-9 April 2006. p. 798-801 
* Hageman NS, Toga AW, Narr K, Shattuck DW (2008).  A diffusion tensor imaging tractography algorithm based on Navier-Stokes fluid mechanics. IEEE Trans. in Medicial Imaging, In Submission.
* Hamilton L, Nuechterlein K, Hageman NS, Woods R, Asarnow R, Alger J, Gaser C, Toga AW, Narr K (2008).  Mean Diffusivity and Fractional Anisotropy as Indicators of Schizophrenia and Genetic Vulnerability, Neuroimage, In Submission.