Difference between revisions of "NA-MIC/Projects/Collaboration/SBIA UPenn"

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(New page: ===Key Investigators=== *Prof. Karol Miller (kmiller at mech.uwa.edu.au) [http://www.mech.uwa.edu.au/ISML/ Lab Webpages], Dr Adam Wittek, Grand Joldes <div style="margin: 20px;"> <div ...)
 
 
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== '''DTI and HARDI analysis tools''' ==
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{|
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|[[Image:ProjectWeek-2008.png|thumb|360px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
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|[[Image:DTIReg.JPG|thumb|420px|The non-linear DTI registration plugin.]]
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|}
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{|
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|[[Image:Registration_example.png|thumb|420px|Example of non-linear DTI registration: Row 1 is the template and row 2 is the average of 10 brains after deformable registration. ]]
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|}
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__NOTOC__
 
===Key Investigators===
 
===Key Investigators===
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*Prof. Karol Miller (kmiller at mech.uwa.edu.au) [http://www.mech.uwa.edu.au/ISML/ Lab Webpages], Dr Adam Wittek, Grand Joldes
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*Ragini Verma, SBIA, UPenn <Ragini.Verma@uphs.upenn.edu>
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*Christos Davatzikos <Christos.Davatzikos@uphs.upenn.edu>
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*Yang Li <Yang.Li@uphs.upenn.edu>  (DTI integration)
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*Luke Bloy <lbloy@seas.upenn.edu>  (HARDI integration)
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*Jinzhong Yang
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*Dinggang Shen
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*Carl-Fredrik Westin, BWH
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*Luis Ibanez, Slicer
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*Steve Pieper, Slicer
  
  
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<h1>Objective</h1>
 
<h1>Objective</h1>
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The Intelligent Systems of Medicine Laboratory (ISML) mission is to work towards improving clinical outcomes through appropriate use of technology. We are interested in biomechanics (both engineering biomechanics and sport biomechanics), biomedical engineering, computer integrated surgery, medical robotics and related fields. We run exciting research projects in these areas, generously funded by The Australian Research Council and other agencies (including NIH).
 
  
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Detailed information about the ISML can be found here [http://www.mech.uwa.edu.au/ISML/]
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To incorporate into Slicer, processing and analysis methods for DTI and HARDI being developed at the Section of Biomedical Image Analysis (SBIA), UPenn [http://www.rad.upenn.edu/sbia]. The main components will be plugins for DTI registration and manifold-based statistics followed by methods for HARDI registration and statistics.
  
 
</div>
 
</div>
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<h1>Approach, Plan</h1>
 
<h1>Approach, Plan</h1>
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*'''DTI registration''': has been developed in SBIA over a period of 2 years, mainly using in-house code (not in ITK). This will be incorporated as a plugin.
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*'''DTI Statistics''': SPM-like package for statistics on the full tensor. The proposed format is again a plugin as it is based on code already existing in SBIA in C, C++.
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*'''HARDI registration''': This is being developed in ITK, building on HARDI representation format currently under development
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*'''HARDI statistics''': being developed in ITK
  
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We intend to contribute to Na-MIC by providing '''algorithms for computing the intra-operative brain deformations''' for image-guided neurosurgery. We treat the brain shift as a continuum mechanics problem involving finite deformations and solve it using non-linear finite element procedures. We use the procedures (non-linear explicit dynamics with Total Lagrangian formulation) that do not require iterations even when applied to non-linear problems and are, therefore, amenable to computing the intra-operative brain deformations in real time (under 150 s) on a standard PC. See also [http://www.mech.uwa.edu.au/ISML/research.htm]
 
 
</div>
 
</div>
  
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<h1>Progress</h1>
 
<h1>Progress</h1>
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*DTI Registration: plugin is ready and was demonstrated
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Two step process:
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1. Executable will be provided immediately (in discussion with : Steve Pieper)
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2.  Source code will be checked in after some licensing issues (as it involves some legacy code) are resolved (in discussion with  : Luis Ibanez) 
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* Tensor Demons registration code was found from Slicer 2.6
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1. Luis Ibanez will be looking at reviving it in discussion with C-F Westin.
  
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2. We will help from our end if recoding is necessary.
  
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*ODF estimation code is ready and will be checked into Namic Sandbox after preliminary testing. This will hopefully serve as the backend to Demian Wasserman's visulaization.
 
</div>
 
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</div>
 
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===References===
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This work was supported in part by NIH grants R01-MH-079938 and R01-MH-070365.
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* Link to [http://www.rad.upenn.edu/sbia  SBIA web site: ]
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* J. Yang, D. Shen, C. Davatzikos and R. Verma, Diffusion Tensor Image Registration Using Tensor Geometry and Orientation Features, in MICCAI 2008, New York.
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* J. Yang, D. Shen, C. Davatzikos and R. Verma, Spatial Normalization of Diffusion Tensor Images Based on Anisotropic Segmentation, in SPIE Medical Imaging 2008, San Diego.
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*  R. Verma, P. Khurd, C. Davatzikos, [https://www.rad.upenn.edu/sbia/papers/181.pdf On Analyzing Diffusion Tensor Images by Identifying Manifold Structure using Isomaps], IEEE Transactions on Medical Imaging, 772-778, Vol. 26, No. 6, 2007
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* P. Khurd, R. Verma and C. Davatzikos, [https://www.rad.upenn.edu/sbia/papers/177.pdf Kernel-based Manifold Learning for Statistical Analysis of Diffusion Tensor Images], Information Processing in Medical Imaging (IPMI), 581-593, Vol. 4584, 2007

Latest revision as of 01:00, 27 June 2008

Home < NA-MIC < Projects < Collaboration < SBIA UPenn

DTI and HARDI analysis tools

Return to Project Week Main Page
The non-linear DTI registration plugin.
Example of non-linear DTI registration: Row 1 is the template and row 2 is the average of 10 brains after deformable registration.

Key Investigators

  • Ragini Verma, SBIA, UPenn <Ragini.Verma@uphs.upenn.edu>
  • Christos Davatzikos <Christos.Davatzikos@uphs.upenn.edu>
  • Yang Li <Yang.Li@uphs.upenn.edu> (DTI integration)
  • Luke Bloy <lbloy@seas.upenn.edu> (HARDI integration)
  • Jinzhong Yang
  • Dinggang Shen
  • Carl-Fredrik Westin, BWH
  • Luis Ibanez, Slicer
  • Steve Pieper, Slicer


Objective

To incorporate into Slicer, processing and analysis methods for DTI and HARDI being developed at the Section of Biomedical Image Analysis (SBIA), UPenn [1]. The main components will be plugins for DTI registration and manifold-based statistics followed by methods for HARDI registration and statistics.

Approach, Plan

  • DTI registration: has been developed in SBIA over a period of 2 years, mainly using in-house code (not in ITK). This will be incorporated as a plugin.
  • DTI Statistics: SPM-like package for statistics on the full tensor. The proposed format is again a plugin as it is based on code already existing in SBIA in C, C++.
  • HARDI registration: This is being developed in ITK, building on HARDI representation format currently under development
  • HARDI statistics: being developed in ITK

Progress

  • DTI Registration: plugin is ready and was demonstrated

Two step process:

1. Executable will be provided immediately (in discussion with : Steve Pieper)

2. Source code will be checked in after some licensing issues (as it involves some legacy code) are resolved (in discussion with : Luis Ibanez)

  • Tensor Demons registration code was found from Slicer 2.6

1. Luis Ibanez will be looking at reviving it in discussion with C-F Westin.

2. We will help from our end if recoding is necessary.

  • ODF estimation code is ready and will be checked into Namic Sandbox after preliminary testing. This will hopefully serve as the backend to Demian Wasserman's visulaization.


References

This work was supported in part by NIH grants R01-MH-079938 and R01-MH-070365.

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