Difference between revisions of "2010 Summer Project Week Implementing OpenCV to Slicer3 for Neuroendoscopic Surgery"

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<gallery>
 
<gallery>
 
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
 
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
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Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.
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Image:sc1.png|SecondaryWindowWithOpenCV module
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Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.
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Image:sc2.png|StereoCalib module</gallery>
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</gallery>
 
  
 
==Key Investigators==
 
==Key Investigators==
 
* Nagoya Institute of Technology: Atsushi Yamada
 
* Nagoya Institute of Technology: Atsushi Yamada
 
* BWH: Nobuhiko Hata, Junichi Tokuda
 
* BWH: Nobuhiko Hata, Junichi Tokuda
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*  Acknowledgement: K. Chinzei (AIST), Y. Hayashi (Nagoya Univ.), M. Komura (Nagoya Institute of Technology), J. Hong (Kyushu Univ.), S.M.Kim, Wang, S. Joung (Univ. of Tokyo), T. Takeuchi (SFC Corp.), H. Liu (BWH), and H. Fujimoto (Nagoya Institute of Technology).
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<div style="margin: 20px;">
 
<div style="margin: 20px;">
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<h3>Objective</h3>
 
<h3>Objective</h3>
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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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The main goal of the OpenCV for nueroendoscopic surgery project is to provide a viewer of the video image as a secondary window of Slicer3 for surgeon as a robot operator. The secondary window can show overlaid volume data on the captured video image and it will be for stereo camera. The developed module will be able to provide the function of the camera calibration for single/stereo camera, too.  
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<h3>Approach, Plan</h3>
 
<h3>Approach, Plan</h3>
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First, we calculate a camera calibration matrix and a compensation vector for lens distortion as XML files by utilizing StereoCalib module. The module is for single/stereo camera.
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In this module, especially for stereo camera, we will develop three types of the secondary window for some uses.
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These types will be changed dinamically.
  
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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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Second, we apply these matrices and vectors of XML format to SecondaryWindowWithOpenCV module for video overlay.
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The position and orientation of the overlaid volume data can be controlled by using OpenIGTLink.  
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Our plan for the project week is to first try out <bar>,...
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SInce this module is for single camera, we will extend it for stereo camera.
  
 
</div>
 
</div>
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<h3>Progress</h3>
 
<h3>Progress</h3>
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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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StereoCalib module for calculation of single/stereo camera calibration matrices and the distortion compensation matrices is now available with only one type secondary window.
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. Single camera calibration (http://files.me.com/slicer2010/od2bbr.mov)
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 +
. Stereo camera calibration (http://files.me.com/slicer2010/2wa8lc.mov)
 +
 
 +
. Dual display test using second and third display for stereo view on Slicer3 (http://files.me.com/slicer2010/2tofam.mov)
 +
 
 +
SecondaryWindowWithOpenCV module is now available only for a single camera as a viewer which can overlay volume data.
 +
 
 +
. Reading camera calibration matrix and distortion compensation vector (http://files.me.com/slicer2010/d27pqr.mov)
  
  
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==Delivery Mechanism==
 
==Delivery Mechanism==
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This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)
 
−
 
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#ITK Module
 
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#Slicer Module
 
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##Built-in
 
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##Extension -- commandline
 
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##Extension -- loadable
 
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#Other (Please specify)
 
  
 
==References==
 
==References==
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*Fletcher P, Tao R, Jeong W, Whitaker R. [http://www.na-mic.org/publications/item/view/634 A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI.] Inf Process Med Imaging. 2007;20:346-358. PMID: 17633712.
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Yamada, A., K. Nishibori, Y. Hayashi, J. Tokuda, N. Hata, K. Chinzei and H. Fujimoto: 3D Slicer Based Surgical Robot Console System, Workshop on Systems and Architectures for Computer Assisted Interventions of the 2009 International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI2009), 2009.
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* Corouge I, Fletcher P, Joshi S, Gouttard S, Gerig G. [http://www.na-mic.org/publications/item/view/292 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Med Image Anal. 2006 Oct;10(5):786-98. PMID: 16926104.
 
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* Corouge I, Fletcher P, Joshi S, Gilmore J, Gerig G. [http://www.na-mic.org/publications/item/view/1122 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Int Conf Med Image Comput Comput Assist Interv. 2005;8(Pt 1):131-9. PMID: 16685838.
 
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* Goodlett C, Corouge I, Jomier M, Gerig G, 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 .
 
  
 
</div>
 
</div>

Latest revision as of 18:41, 22 June 2010

Home < 2010 Summer Project Week Implementing OpenCV to Slicer3 for Neuroendoscopic Surgery

  • SecondaryWindowWithOpenCV module

  • StereoCalib module

Key Investigators

  • Nagoya Institute of Technology: Atsushi Yamada
  • BWH: Nobuhiko Hata, Junichi Tokuda
  • Acknowledgement: K. Chinzei (AIST), Y. Hayashi (Nagoya Univ.), M. Komura (Nagoya Institute of Technology), J. Hong (Kyushu Univ.), S.M.Kim, Wang, S. Joung (Univ. of Tokyo), T. Takeuchi (SFC Corp.), H. Liu (BWH), and H. Fujimoto (Nagoya Institute of Technology).


Objective

The main goal of the OpenCV for nueroendoscopic surgery project is to provide a viewer of the video image as a secondary window of Slicer3 for surgeon as a robot operator. The secondary window can show overlaid volume data on the captured video image and it will be for stereo camera. The developed module will be able to provide the function of the camera calibration for single/stereo camera, too.




Approach, Plan

First, we calculate a camera calibration matrix and a compensation vector for lens distortion as XML files by utilizing StereoCalib module. The module is for single/stereo camera. In this module, especially for stereo camera, we will develop three types of the secondary window for some uses. These types will be changed dinamically.

Second, we apply these matrices and vectors of XML format to SecondaryWindowWithOpenCV module for video overlay. The position and orientation of the overlaid volume data can be controlled by using OpenIGTLink. SInce this module is for single camera, we will extend it for stereo camera.

Progress

StereoCalib module for calculation of single/stereo camera calibration matrices and the distortion compensation matrices is now available with only one type secondary window.

. Single camera calibration (http://files.me.com/slicer2010/od2bbr.mov)

. Stereo camera calibration (http://files.me.com/slicer2010/2wa8lc.mov)

. Dual display test using second and third display for stereo view on Slicer3 (http://files.me.com/slicer2010/2tofam.mov)

SecondaryWindowWithOpenCV module is now available only for a single camera as a viewer which can overlay volume data.

. Reading camera calibration matrix and distortion compensation vector (http://files.me.com/slicer2010/d27pqr.mov)


Delivery Mechanism

References

Yamada, A., K. Nishibori, Y. Hayashi, J. Tokuda, N. Hata, K. Chinzei and H. Fujimoto: 3D Slicer Based Surgical Robot Console System, Workshop on Systems and Architectures for Computer Assisted Interventions of the 2009 International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI2009), 2009.

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