Difference between revisions of "2008 Winter Project Week GroupwiseReg"

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<h1>Objective</h1>
 
<h1>Objective</h1>
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We have developed techniques for finding the optimal geodesic path (or anchor tract) between two regions of interest in DWMRI data.
 
  
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The objectives of this project are to port the Fast Sweeping and optimal geodesic path tractography code to ITK as well as the code to provide for volumetric segmentation of DW-MRI data.
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The goal of this project is to expand the NAMIC Software Kit with the addition of an image-based atlas
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building algorithm that was developed by Polina Golland’s lab at MIT. The basic functionality of this software will
 +
be demonstrated to the NAMIC community at the January 2008 NAMIC all-hands meeting. A secondary
 +
goal is to begin the process of gathering usability and interface requests from targeted clinical collaborators.
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It is intended that users’ requests will be incorporated in to a future project aimed at tailoring this software
 +
for widespread NAMIC use.
  
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See our [[Algorithm:GATech:Finsler_Active_Contour_DWI| Project Page]] for more details.
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See our [[Projects:GroupwiseRegistration| Algorithm Project Page]] for more details.
  
 
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<h1>Approach, Plan </h1>
 
<h1>Approach, Plan </h1>
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Our approach is described by the references below.  Our challenge is to build the ITK infrastructure (such as new ITK iterators) to support this algorithm. Our main purpose at the Project Week is to collaborate on new algorithms and clinical data to provide the best solutions for our DBP partners.
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 +
The registration algorithms are already available as C++ sourcecode.  We plan to integrate them into the NAMIC community by:
 +
 
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*Adapt sourcecode to utilize the command-line parsing mechanism that was designed for Slicer3 external modules.
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*Create a simple Slicer3 graphical user interface (external module) that allows a user to generate an atlas from their data.
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*User Feedback. During the January 2008 NAMIC all-hands meeting we will solicit feedback on this project from potential collaborators.
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</div>
 
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<h1>Progress</h1>
 
<h1>Progress</h1>
  
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====June 2007 Project Week====
 
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During this Project Week, we did a lot of algorithmic design work, focusing on leveraging optimal or geodesic path information to provide for volumetric segmentations of fiber bundles.  Working with Marek Kubicki and the Harvard DBP, we were able to begin the process of applying our algorithm to the full cingulum bundle with new labelmaps and to a new fiber bundle - Arcuate.  We have recently achieved significant results in volumetric segmentations using a locally-constrained region-based technique (see the images above).
 
  
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====Jan 2007 Project Half Week====
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====Jan 2008 Project Week====
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We finished the itkDirectionalIterator which will be needed in the Fast Sweeping implementation.  Furthermore, we made progress in porting our Matlab code to ITK.
 
  
 
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===References===
 
===References===
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* J. Melonakos, M. Niethammer, V. Mohan, M. Kubicki, J. Miller, A. Tannenbaum. Locally-Constrained Region-Based Methods for DW-MRI Segmentation. Submitted to MMBIA 2007.
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* S.K. Balci, P. Golland, M.E. Shenton, W.M. Wells III. Free-Form B-spline Deformation Model for Groupwise Registration. In Proceedings of MICCAI 2007 Statistical Registration Workshop: Pair-wise and Group-wise Alignment and Atlas Formation, 23-30, 2007.
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* V. Mohan, J. Melonakos, M. Niethammer, M. Kubicki, and A. Tannenbaum. Finsler Level Set Segmentation for Imagery in Oriented Domains. BMVC 2007.
 
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* J. Melonakos, V. Mohan, M. Niethammer, K. Smith, M. Kubicki, and A. Tannenbaum. Finsler Tractography for White Matter Connectivity Analysis of the Cingulum Bundle. MICCAI 2007.
 
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* J. Melonakos, E. Pichon, S. Angenet, and A. Tannenbaum. Finsler Active Contours. IEEE Transactions on Pattern Analysis and Machine Intelligence, to appear in 2007.
 
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* E. Pichon and A. Tannenbaum. Curve segmentation using directional information, relation to pattern detection. In IEEE International Conference on Image Processing (ICIP), volume 2, pages 794-797, 2005.
 
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* E. Pichon, C-F Westin, and A. Tannenbaum. A Hamilton-Jacobi-Bellman approach to high angular resolution diffusion tractography. In International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), pages 180-187, 2005.
 

Latest revision as of 15:17, 11 January 2008

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Figure 1: On the left is shown a stack of images and a sample pixel stack around a cortical region. On the left is shown the Gaussian(blue) fittet to a real sample from the dataset we used along with the non-parametric density estimate(red). Note that the distribution is bi-modal because of white matter-gray matter transaction.


Key Investigators

  • MIT: Serdar Balci, Polina Golland
  • Kitware: Brad Davis
  • SCI: Casey Goodlett

Objective

The goal of this project is to expand the NAMIC Software Kit with the addition of an image-based atlas building algorithm that was developed by Polina Golland’s lab at MIT. The basic functionality of this software will be demonstrated to the NAMIC community at the January 2008 NAMIC all-hands meeting. A secondary goal is to begin the process of gathering usability and interface requests from targeted clinical collaborators. It is intended that users’ requests will be incorporated in to a future project aimed at tailoring this software for widespread NAMIC use.

See our Algorithm Project Page for more details.

Approach, Plan

The registration algorithms are already available as C++ sourcecode. We plan to integrate them into the NAMIC community by:

  • Adapt sourcecode to utilize the command-line parsing mechanism that was designed for Slicer3 external modules.
  • Create a simple Slicer3 graphical user interface (external module) that allows a user to generate an atlas from their data.
  • User Feedback. During the January 2008 NAMIC all-hands meeting we will solicit feedback on this project from potential collaborators.

Progress


Jan 2008 Project Week



References

  • S.K. Balci, P. Golland, M.E. Shenton, W.M. Wells III. Free-Form B-spline Deformation Model for Groupwise Registration. In Proceedings of MICCAI 2007 Statistical Registration Workshop: Pair-wise and Group-wise Alignment and Atlas Formation, 23-30, 2007.
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