2009 Winter Project Week Hageman FMTractography - Revision history

Nhageman at 16:56, 4 June 2009

2009-06-04T16:56:19Z

Nhageman: /* Key Investigators */

2009-01-09T17:51:29Z

Key Investigators

Nhageman: /* Key Investigators */

2009-01-09T17:50:38Z

Key Investigators

Nhageman: /* Key Investigators */

2009-01-09T17:27:30Z

Key Investigators

Nhageman: /* Key Investigators */

2009-01-09T17:06:53Z

Key Investigators

Nhageman: /* Key Investigators */

2009-01-05T09:04:02Z

Key Investigators

Nhageman at 09:00, 5 January 2009

2009-01-05T09:00:26Z

Nhageman at 08:59, 5 January 2009

2009-01-05T08:59:12Z

Pieper: /* Key Investigators */

2008-12-21T19:59:48Z

Key Investigators

Nhageman: New page: {| |Project Week Main Page ]] |[[Image:Hageman_cspfig4NAMIC_07-06-22.png|thumb|320px|Corticospinal tracts segmented...

2008-12-11T22:05:36Z

New page: {| |thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page ]] |[[Image:Hageman_cspfig4NAMIC_07-06-22.png|thumb|320px|Corticospinal tracts segmented...

New page

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_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.]]
|}

__NOTOC__

===Key Investigators===
* UCLA: Nathan Hageman
* UCLA: Arthur Toga, Ph.D

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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>
* Pre-computed implementation of fluid animation in VTK successful. We will now streamline the method for real time animation.
* Layout for Slicer 3 plugin complete. We will include analysis and GUI code in Slicer code repository after final validation.
* 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===
* 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.

@@ Line 47: / Line 47: @@
 <h1>Progress</h1>
-* Command line fluid mechanics tractography module integrated into Slicer 3.
+* 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.

@@ Line 48: / Line 48: @@
 <h1>Progress</h1>
 * Command line fluid mechanics tractography module integrated into Slicer 3.
-* VTK module for fluid mechanics visualization completed and to be included in next Slicer release.
+* VTK module for fluid mechanics visualization completed.
-* Arrangements made to include FM tractography as part of DTI validation effort.
+** Discussion of possibly including module in next stable Slicer release.
 </div>

@@ Line 48: / Line 48: @@
 <h1>Progress</h1>
 * Command line fluid mechanics tractography module integrated into Slicer 3.
-* vtk module for fluid mechanics visualization completed and to be included in next Slicer release.
+* VTK module for fluid mechanics visualization completed and to be included in next Slicer release.
+* Arrangements made to include FM tractography as part of DTI validation effort.
 </div>

@@ Line 47: / Line 47: @@
 <h1>Progress</h1>
 * Command line fluid mechanics tractography module integrated into Slicer 3.
 </div>

@@ Line 3: / Line 3: @@
 |[[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:Hageman_FMModuleScreenshot.png|thumb|320px|Screenshot of Slicer Module for Fluid Mechanics Tractography.]]
+|[[Image:FMModuleScreenshot.png|thumb|320px|Screenshot of Slicer Module for Fluid Mechanics Tractography.]]
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 {|
-|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
+|[[Image:PW2009-v3.png|thumb|320px|[[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.]]

← Older revision		Revision as of 19:59, 21 December 2008
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	* UCLA: Nathan Hageman		* UCLA: Nathan Hageman
	* UCLA: Arthur Toga, Ph.D		* UCLA: Arthur Toga, Ph.D
		+	* Isomics: Steve Pieper and Alex Yarmarkovich