NA-MIC/Projects/Collaboration/3D Ultrasound Module in Slicer3 - Revision history

Purang: /* Key Investigators */

2008-06-27T20:27:37Z

Key Investigators

Dgobbi: /* Key Investigators */

2008-06-27T13:45:13Z

Key Investigators

Dpace at 11:42, 27 June 2008

2008-06-27T11:42:51Z

Dgobbi: /* Key Investigators */

2008-06-11T21:21:17Z

Key Investigators

Dgobbi: /* Key Investigators */

2008-06-11T21:20:54Z

Key Investigators

Dgobbi: /* Key Investigators */

2008-06-11T21:20:21Z

Key Investigators

Dpace at 20:39, 11 June 2008

2008-06-11T20:39:29Z

Dpace: New page: {| |Project Week Main Page ]] |[[Image:genuFAp.jpg|thumb|320px|Scatter plot of the original FA data through ...

2008-06-11T20:17:42Z

New page: {| |thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page ]] |[[Image:genuFAp.jpg|thumb|320px|Scatter plot of the original FA data through ...

New page

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:genuFAp.jpg|thumb|320px|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.]]
|[[Image:genuFA.jpg|thumb|320px|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.]]
|}

__NOTOC__

===Instructions for Use of this Template===
#Please create a new wiki page with an appropriate title for your project using the convention NA-MIC/Projects/Theme-Name/Project-Name
#Copy the entire text of this page into the page created above
#Link the created page into the list of projects for the project event
#Delete this section from the created page
#Send an email to tkapur at bwh.harvard.edu if you are stuck

===Key Investigators===
* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig
* Utah: Tom Fletcher, Ross Whitaker

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<h1>Objective</h1>
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>Approach, Plan</h1>

Our approach for analyzing diffusion tensors is summarized in the IPMI 2007 reference below. The main challenge to this approach is <foo>.

Our plan for the project week is to first try out <bar>,...
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<h1>Progress</h1>

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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===References===
* 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.
* 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.
* 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
* 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 .

@@ Line 9: / Line 9: @@
 * SPL:  Junichi Tokuda, Haiying Liu, Benjamin Grauer, Noby Hata
 * SJTU, Shanghai:  Ziying Jiang, Qingfeng Jin, Tingting Xi, Shuqin Ding, Yan Sun, Lixu Gu
-* Queen's:  David Gobbi, Siddharth Vikal
+* Queen's:  Jonathan Boisvert, David Gobbi, Siddharth Vikal, Purang Abolmaesumi
 * Robarts:  Danielle Pace, Terry Peters
 * Present at the NA-MIC programming week:  Junichi, Haiying, Noby, David, Siddharth, Danielle

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 ** vtkVideoSource, vtkVideoBuffer and vtkVideoFrame classes are completed but not tested
 ** we outlined the mechanism for integrating cardiac gating into the current reconstruction framework, but it is not coded yet
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← Older revision		Revision as of 11:42, 27 June 2008
Line 41:		Line 41:

	<h1>Progress</h1>		<h1>Progress</h1>
		+	* For accurate ECG-gating, the patient's heart rate must not change during a single cardiac cycle - this is because phase-detection uses only the patient's heart rate and the time since the beginning of the cardiac cycle. We plan to ensure that the heart rate measurement is valid by "buffering" the incoming images so that they are inserted into the volume 1-2 seconds after being read from the video source. However, we discovered that the current vtkVideoSource mechanism doesn't allow you to "seek" and "record" at the same time.
		+	* This week, we have been restructuring the vtkVideoSource class so that its frame buffer and frames are stored in a separate class. This restructuring will allow us to access old frames while the video source is still recording.
		+	* Progress this week:
		+	** vtkVideoSource, vtkVideoBuffer and vtkVideoFrame classes are completed but not tested
		+	** we outlined the mechanism for integrating cardiac gating into the current reconstruction framework, but it is not coded yet

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@@ Line 22: / Line 22: @@
 * reconstruct 3D ultrasound volumes from multiple tracked 2D images
 * reconstruct 4D ultrasound volumes from multiple tracked 2D images with ECG-gating
-* reconstruct panoramic 3D ultrasound volumes from multiple tracked 3D images
+* reconstruct panoramic 3D ultrasound volumes from multiple tracked 3D images on a wide variety of ultrasound scanners
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 During the project week,
-# The Queen's group will interface their SonixRP ultrasound acquisition pipeline to Slicer3 via OpenIGTLink with the help of Junichi and Noby
+* The Queen's group will interface their SonixRP ultrasound acquisition pipeline to Slicer3 via OpenIGTLink with the help of Junichi and Noby
-# Danielle will work with David to fix up the last bugs in the freehand 3D reconstruction code and to add the ECG-gating functionality.
+* Danielle will work with David to fix up the last bugs in the freehand 3D reconstruction code and to add the ECG-gating functionality.
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 |[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
 |}
 __NOTOC__
 ===Key Investigators===
-* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig
+* SPL:  Junichi Tokuda, Haiying Liu, Benjamin Grauer, Noby Hata
-* Utah: Tom Fletcher, Ross Whitaker
+* SJTU, Shanghai:  Ziying Jiang, Qingfeng Jin, Tingting Xi, Shuqin Ding, Yan Sun, Lixu Gu
@@ Line 25: / Line 19: @@
 <h1>Objective</h1>
-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.
+We are working on a 3D ultrasound module in Slicer3, with the goal of creating a module that can
+* reconstruct 3D ultrasound volumes from multiple tracked 2D images
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@@ Line 34: / Line 31: @@
 <h1>Approach, Plan</h1>
-Our approach for analyzing diffusion tensors is summarized in the IPMI 2007 reference below.  The main challenge to this approach is <foo>.
+D ultrasound volumes can be created from 2D ultrasound images by acquiring multiple 2D images while tracking the probe.  The tracking information is used to insert the images in the correct position and orientation within the 3D volume.  A time series of 3D ultrasound volumes (4D US) can be created by incorporating ECG-gating:  the 2D ultrasound images are inserted into the correct volume using the ECG information.  Finally, panoramic 3D ultrasound volumes can also be built up from smaller 3D ultrasound volumes by simply tracking the probe.
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 <h1>Progress</h1>
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 ===References===
-* 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.
+See the 3D ultrasound module wiki page at http://www.na-mic.org/Wiki/index.php/3D_Ultrasound_Module_in_Slicer_3