Difference between revisions of "2009 Winter Project Week Hageman UCLANSBrainLab"

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|[[Image:Hageman_cspfig4NAMIC_07-06-22.png|thumb|320px|Corticospinal tracts segmented using our fluid mechanics based tractography method.]]
 
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<h1>Objective</h1>
 
<h1>Objective</h1>
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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.
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Preoperative mapping of the brain is an important step in tumor resection involving functionally critical areas of the brain.  Visualization of the location of gray and white matter structures with respect to the tumor mass helps the surgeon plan an operative approach that will minimize post-operative deficits.  While functional areas have successfully been localized via fMRI, recently diffusion tensor imaging (DTI) has been shown to be successful in localizing critical white matter structures.  The neurosurgery department at UCLA has been using BrainLab to do this type of preoperative planning in tumor patients.  The recent link of BrainLab to Slicer allows us to take advantage of the alogithms in Slicer in the clinical research setting.  The goal of this project is to develop a successful link between BrainLab and Slicer for the UCLA neurosugery department to assist in preoperative planning of tumor resection.
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See our [[hageman:NAMICFluidMechDTITractography|Project Page]] for more information.
 
  
 
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<h1>Approach, Plan</h1>
 
<h1>Approach, Plan</h1>
  
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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:
 
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* 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:
 
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**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.
 
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**computation of fluid velocity vector field volume
 
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**reconstruction of tracts based on the above fluid velocity volume
 
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** Optimizing initial coding of method in ITK (better use of multithreading)
 
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** Specialized visualization using VTK:
 
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*** Fluid velocity vector field animation
 
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*** Layout for Slicer 3 Plug-in
 
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*** Interactive (real-time) manipulation of sources/sinks (ROIs) on steady-state fluid solution (possible application for intra-operative DTI)
 
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* 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>
 
<h1>Progress</h1>
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* Pre-computed implementation of fluid animation in VTK successful.  We will now streamline the method for real time animation.
 
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* Layout for Slicer 3 plugin complete.  We will include analysis and GUI code in Slicer code repository after final validation.
 
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* Initial analysis of lupus lesion data from MIND institute completed but noise from data has created too many false positive vortices.  We will work to make our method more robust.
 
  
 
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===References===
 
===References===
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* 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
 
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* 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.
 
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* 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.
 

Revision as of 13:16, 18 December 2008

Home < 2009 Winter Project Week Hageman UCLANSBrainLab
Return to Project Week Main Page



Key Investigators

  • UCLA: Nathan Hageman
  • UCLA: Arthur Toga, Ph.D


Objective

Preoperative mapping of the brain is an important step in tumor resection involving functionally critical areas of the brain. Visualization of the location of gray and white matter structures with respect to the tumor mass helps the surgeon plan an operative approach that will minimize post-operative deficits. While functional areas have successfully been localized via fMRI, recently diffusion tensor imaging (DTI) has been shown to be successful in localizing critical white matter structures. The neurosurgery department at UCLA has been using BrainLab to do this type of preoperative planning in tumor patients. The recent link of BrainLab to Slicer allows us to take advantage of the alogithms in Slicer in the clinical research setting. The goal of this project is to develop a successful link between BrainLab and Slicer for the UCLA neurosugery department to assist in preoperative planning of tumor resection.

Approach, Plan

Progress


References

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