Difference between revisions of "NA-MIC/Projects/Collaboration/3D Ultrasound Module in Slicer3"

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|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
 
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|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__
 
__NOTOC__
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===Instructions for Use of this Template===
 
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#Please create a new wiki page with an appropriate title for your project using the convention NA-MIC/Projects/Theme-Name/Project-Name
 
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#Copy the entire text of this page into the page created above
 
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#Link the created page into the list of projects for the project event
 
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#Delete this section from the created page
 
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#Send an email to tkapur at bwh.harvard.edu if you are stuck
 
  
 
===Key Investigators===
 
===Key Investigators===
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* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig
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* SPL: Junichi Tokuda, Haiying Liu, Benjamin Grauer, Noby Hata
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* Utah: Tom Fletcher, Ross Whitaker
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* SJTU, Shanghai:  Ziying Jiang, Qingfeng Jin, Tingting Xi, Shuqin Ding, Yan Sun, Lixu Gu
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* Queen's:  David Gobbi
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* Robarts:  Danielle Pace, Terry Peters
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* Present at the NA-MIC programming week: Junichi, Haiying, Noby, David, Danielle
  
  
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<h1>Objective</h1>
 
<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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We are working on a 3D ultrasound module in Slicer3, with the goal of creating a module that can
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* reconstruct 3D ultrasound volumes from multiple tracked 2D images
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* reconstruct 4D ultrasound volumes from multiple tracked 2D images with ECG-gating
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* reconstruct panoramic 3D ultrasound volumes from multiple tracked 3D images
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on a wide variety of ultrasound scanners
  
 
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<h1>Approach, Plan</h1>
 
<h1>Approach, Plan</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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3D 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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During the project week, David will work with Junichi and Noby to interface OpenIGTLink with the freehand 3D reconstruction code.  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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Our plan for the project week is to first try out <bar>,...
 
 
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<h1>Progress</h1>
 
<h1>Progress</h1>
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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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===References===
 
===References===
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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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See the 3D ultrasound module wiki page at http://www.na-mic.org/Wiki/index.php/3D_Ultrasound_Module_in_Slicer_3
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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 .
 

Revision as of 20:39, 11 June 2008

Home < NA-MIC < Projects < Collaboration < 3D Ultrasound Module in Slicer3
Return to Project Week Main Page



Key Investigators

  • 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
  • Robarts: Danielle Pace, Terry Peters
  • Present at the NA-MIC programming week: Junichi, Haiying, Noby, David, Danielle


Objective

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
  • reconstruct 4D ultrasound volumes from multiple tracked 2D images with ECG-gating
  • reconstruct panoramic 3D ultrasound volumes from multiple tracked 3D images

on a wide variety of ultrasound scanners

Approach, Plan

3D 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.

During the project week, David will work with Junichi and Noby to interface OpenIGTLink with the freehand 3D reconstruction code. Danielle will work with David to fix up the last bugs in the freehand 3D reconstruction code and to add the ECG-gating functionality.

Progress



References

See the 3D ultrasound module wiki page at http://www.na-mic.org/Wiki/index.php/3D_Ultrasound_Module_in_Slicer_3

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