Difference between revisions of "User talk:Nhageman"
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| + | |[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]] | ||
| + | |valign="top"|[[Image:Hageman_cspfig4NAMIC_07-06-22.png|thumb|320px|Corticospinal tracts segmented using our fluid mechanics based tractography method.]] | ||
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| + | __NOTOC__ | ||
| + | ===Key Investigators=== | ||
| + | * Georgia Tech: John Melonakos, Vandana Mohan | ||
| + | * Kitware: Luis Ibanez | ||
| + | * BWH: Mark Niethammer, Marek Kubicki | ||
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| + | <div style="margin: 20px;"> | ||
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| + | <div style="width: 27%; float: left; padding-right: 3%;"> | ||
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| + | <h1>Objective</h1> | ||
| + | We have developed techniques for finding the optimal geodesic path (or anchor tract) between two regions of interest in DWMRI data. | ||
| + | |||
| + | 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. | ||
| + | |||
| + | See our [[Algorithm:GATech:Finsler_Active_Contour_DWI| Project Page]] for more details. | ||
| + | |||
| + | </div> | ||
| + | |||
| + | <div style="width: 27%; float: left; padding-right: 3%;"> | ||
| + | |||
| + | <h1>Approach, Plan </h1> | ||
| + | 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. | ||
| + | </div> | ||
| + | |||
| + | <div style="width: 40%; float: left;"> | ||
| + | |||
| + | <h1>Progress</h1> | ||
| + | |||
| + | ====June 2007 Project Week==== | ||
| + | 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). | ||
| + | |||
| + | ====Jan 2007 Project Half Week==== | ||
| + | We finished the itkDirectionalIterator which will be needed in the Fast Sweeping implementation. Furthermore, we made progress in porting our Matlab code to ITK. | ||
| + | |||
| + | </div> | ||
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| + | <br style="clear: both;" /> | ||
| + | |||
| + | </div> | ||
| + | |||
| + | |||
| + | ===References=== | ||
| + | * 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. | ||
| + | * V. Mohan, J. Melonakos, M. Niethammer, M. Kubicki, and A. Tannenbaum. Finsler Level Set Segmentation for Imagery in Oriented Domains. BMVC 2007. | ||
| + | * 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. | ||
| + | * J. Melonakos, E. Pichon, S. Angenet, and A. Tannenbaum. Finsler Active Contours. IEEE Transactions on Pattern Analysis and Machine Intelligence, to appear in 2007. | ||
| + | * 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. | ||
| + | * 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. | ||
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|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]] | |[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]] | ||
Revision as of 20:24, 18 December 2007
Home < User talk:Nhageman Return to 2008_Winter_Project_Week |
Key Investigators
- Georgia Tech: John Melonakos, Vandana Mohan
- Kitware: Luis Ibanez
- BWH: Mark Niethammer, Marek Kubicki
Objective
We have developed techniques for finding the optimal geodesic path (or anchor tract) between two regions of interest in DWMRI data.
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.
See our Project Page for more details.
Approach, Plan
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.
Progress
June 2007 Project Week
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).
Jan 2007 Project Half Week
We finished the itkDirectionalIterator which will be needed in the Fast Sweeping implementation. Furthermore, we made progress in porting our Matlab code to ITK.
References
- 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.
- V. Mohan, J. Melonakos, M. Niethammer, M. Kubicki, and A. Tannenbaum. Finsler Level Set Segmentation for Imagery in Oriented Domains. BMVC 2007.
- 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.
- J. Melonakos, E. Pichon, S. Angenet, and A. Tannenbaum. Finsler Active Contours. IEEE Transactions on Pattern Analysis and Machine Intelligence, to appear in 2007.
- 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.
- 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.
 Return to Project Week Main Page |
Key Investigators
- UCLA: Nathan Hageman
- UCLA: Arthur Toga, Ph.D
- Georgia Tech: John Melonakos (interested collaborator)
Objective
We have developed a diffusion tensor imaging (DTI) tractography method based on Navier-Stokes fluid mechanics. The goal of this project is to make our method compatible with NA-MIC ITK-based software infrastructure in order facilitate its dissemination to the scientific community.
Approach, Plan
The details of our method is given in the paper listed in the reference section. Our approach will focus on working with NA-MIC members and collaborators to successfully reimplement our method in a NA-MIC ITK compatible form. Our plan for the project week is to introduce the basics of our method to the NA-MIC community and make progress in converting our code to a compatible form.
Progress
We have made progress in converting our DTI analysis code to work in the ITK/vTK environment. We have created modules for
- reconstruction of the diffusion tensor and computation of common DTI scalar volumes (FA, LI, RGB)
- computation of fluid velocity vector field volume
- reconstruction of tracts based on the above fluid velocity volume
Current work is focusing on optimizing the code for the above modules and integrating them as tools in NAMIC's Slicer software environment.
References
- NS Hageman, DW Shattuck, K Narr, AW Toga. A Diffusion tensor imaging tractography method based on Navier-Stokes Fluid Mechanics. In Proceedings of the 2006 IEEE International Symposium on Biomedical Imaging, 2006.
