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National Alliance-Medical Imaging Computing (NAMIC) U54-EB005149

The National Alliance for Medical Imaging Computing (NAMIC) is a multi-institutional, interdisciplinary team of computer scientists, software engineers, and medical investigators who develop computational tools for the analysis and visualization of medical image data. The purpose of the center is to provide the infrastructure and environment for the development of computational algorithms and open source technologies and to oversee training and dissemination of these tools to the medical research community. This world-class software and development environment serves as a foundation for accelerating the development and deployment of computational tools that are readily accessible to the medical research community.

The team combines cutting-edge computer vision research (to create medical imaging analysis algorithms) with state-of-the-art software engineering techniques (based on "extreme" programming techniques in a distributed, open-source environment) to enable computational examination of both basic neuroscience and neurological disorders. Driving biological projects will come initially from the study of schizophrenia, but the methods will be applicable to many other diseases. Therefore, computational tools and open systems technologies and platforms developed by NAMIC will initially be used to study anatomical structures and connectivity patterns in the brain, derangements of which have long been thought to play a role in the etiology of schizophrenia.

The release in the past year of the Slicer IGT NeuroNav module with real-time DTI tractography functionality is a direct result of collaboration with NA-MIC and the NCIGT. The software infrastructure for computing fiber tracts was created by the NA-MIC Engineering core, while the neurosurgical planning workflow was created and used clinically by the NCIGT Computation and Neurosurgery Cores.

Publications

• Tokuda J, Yaniv Z. OpenIGTLink. In IGSTK Image-Guided Surgery Toolkit: An Open-Source C++ Library (Kevin Cleary, Patrick Cheng, Andinet Enquobahrie and Ziv Yaniv eds.) 2009; 257-265.

• O'Donnell L, Westin C, Golby A. Tract-based morphometry for white matter group analysis. Neuroimage. 2009 Apr 15;45(3):832-44. PMID: 19154790.

• Pace D, Oguro S, Haker S, Hata N. MR-guided prostate interventions with 3D Slicer and the NA-MIC Kit. NCIGT-SNR Tutorial. 2009 January;

• Tie Y, Suarez R, Whalen S, Radmanesh A, Norton I, Golby A. Comparison of blocked and event-related fMRI designs for pre-surgical language mapping. Neuroimage. 2008 Dec 6. PMID: 19101639.

• Xia T, Baird C, Jallo G, Hayes K, Nakajima N, Hata N, Kazanzides P. An integrated system for planning, navigation and robotic assistance for skull base surgery. Int J Med Robot. 2008 Dec;4(4):321-30. PMID: 18803337.

• Pace D, Hata N. Image Guided Therapy in Slicer3: Planning for Image Guided Neurosurgery. NCIGT-SNR Tutorial. 2008 November;

• Poynton C, Jenkinson M, Whalen S, Golby A, Wells III W. Fieldmap-Free Retrospective Registration and Distortion Correction for EPI-Based Functional Imaging. Int Conf Med Image Comput Comput Assist Interv. 2008;11(Pt 2):271-279. PMID: 18982615.

• Tokuda J, Fischer G, Csoma C, DiMaio S, Gobbi D, Fichtinger G, Tempany C, Hata N. Software Strategy for Robotic Transperineal Prostate Therapy in Closed-Bore MRI. Int Conf Med Image Comput Comput Assist Interv. 2008;11(Pt 2):701-709. PMID: 18982666.

• Pace D, Tokuda J, Liu H, Hata N. Image Guided Therapy in Slicer3: Introduction to Navigation using OpenIGTLink. NCIGT-SNR Tutorial. 2008 June;

• Maddah M, Zollei L, Grimson W, Wells W. Modeling of Anatomical Information in Clustering of White Matter Fiber Trajectories Using Dirichlet Distribution. IEEE Workshop on Mathematical Methods in Biomedical Image Analysis. 2008;

• Mewes P, Tokuda J, DiMaio S, Fischer G, Csoma C, Gobbi D, Tempany C, Fichtinger G, Hata N. Integrated System for Robot-Assisted in Prostate Biopsy in Closed MRI Scanner. Proceedings of the IEEE International Conference on Robotics and Automation 2008; 2959-2962.

• Konukoglu E, Wells W, Novellas S, Ayache N, Kikinis R, P. M. Black , Pohl K. Monitoring Slowly Evolving Tumors. Proceedings of the 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro 2008; 812-815.

• Maddah M, Zöllei L, Grimson W, Westin C, Wells W. A Mathematical Framework for Incorporating Anatomical Knowledge in DT-MRI Analysis. Proceedings of the 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro 2008; 4543943: 105–108. PMID: 19212449. PMCID: PMC2638065.

• Maddah M, Grimson WEL, Warfield SK, Wells WM. A unified framework for clustering and quantitative analysis of white matter fiber tracts. Med Image Anal. 2008 Apr;12(2):191-202. PMID: 18180197.

• Tempany CMC, Straus S, Hata N, Haker S. MR-guided prostate interventions. J Magn Reson Imaging, 2008 Feb;27(2):356-67. PMID: 18219689.

• Kindlmann G, Ennis D, Whitaker R, Westin C. Diffusion tensor analysis with invariant gradients and rotation tangents. IEEE Trans Med Imaging. 2007 Nov;26(11):1483-99. PMID: 18041264.

• Fan A, Fisher III JW, Wells III W, Levitt JJ, Willsky AS. MCMC Curve Sampling for Image Segmentation. Int Conf Med Image Comput Comput Assist Interv. 2007;10(Pt 2):477-485. PMID: 18044603.

• Pohl KM, Fisher J, Bouix S, Shenton M, McCarley R, Grimson E, Kikinis R, Wells W. Using the logarithm of odds to define a vector space on probabilistic atlases. Med Image Anal. 2007 Oct;11(5):465-77. PMID: 17698403.

• Hata N, Piper S, Jolesz F, Tempany C, Black P, Morikawa S, Iseki H, Hashizume M, Kikinis R. Application of Open Source Image Guided Therapy Software in MR-guided Therapies. Int Conf Med Image Comput Comput Assist Interv. 2007;10(Pt 1):491-8. PMID: 18051095.

• O'Donnell L, Westin CF, Golby AJ. Tract-Based Morphometry. Int Conf Med Image Comput Comput Assist Interv. 2007;10(Pt 2):161-168. PMID: 18044565.

• DiMaio SP, Kapur T, Cleary K, Aylward S, Kazanzides P, Vosburgh K, Ellis R, Duncan J, Farahani K, Lemke H, Peters T, Lorensen W, Gobbi D, Haller J, Clarke L, Pizer S, Taylor R, Galloway Jr R, Fichtinger G, Hata N, Lawson K, Tempany C, Kikinis R, Jolesz F. Challenges in image-guided therapy system design. NeuroImage 2007; 37(Suppl 1):S144-S151. PMID: 17644360.

• Dauguet J, Peled S, Berezovskii V, Delzescaux T, Warfield SK, Born R, Westin C. Comparison of fiber tracts derived from in-vivo DTI tractography with 3D histological neural tract tracer reconstruction on a macaque brain. Neuroimage. 2007 Aug 15;37(2):530-8. PMID: 17604650.

• Pohl KM, Kikinis R, Wells WM. Active mean fields: solving the mean field approximation in the level set framework. Inf Process Med Imaging. 2007;20:26-37.PMID: 17633686.

• Maddah M, Wells WM, Warfield SK,Westin CF, Grimson WEL. Probabilistic clustering and quantitative analysis of white matter fiber tracts. Inf Process Med Imaging. 2007;20:372-83. PMID: 17633714.

• Nain D, Haker S, Bobick S, Tannenbaum A.Multiscale 3-D shape representation and segmentation using spherical wavelets. IEEE Trans Med Imaging. 2007 Apr;26(4):598-618. PMID: 17427745.

• Nain D, Haker S, Bobick A, Tannenbaum A. Shape-Driven 3D Segmentation Using Spherical Wavelets. Int Conf Med Image Comput Comput Assist Interv. 2006;9(Pt 1):66-74. PMID: 17354875.

• Dauguet J, Peled S,Berezovskii V, Delzescaux T, Warfield SK, Born R, Westin C. 3D Histological Reconstruction of Fiber Tracts and Direct Comparison with Diffusion Tensor MRI Tractography. Int Conf Med Image Comput Comput Assist Interv.2006;9(Pt 1):109-16. PMID: 17354880.

• DiMaio SP, Archip N, Hata N, Talos I, Warfield SK, Majumdar A, Mcdannold N, Hynynen K, Morrison PR, Wells WM, Kacher DF,Ellis RE, Golby AJ, Black PM, Jolesz FA, Kikinis R. Image guided Neurosurgery at Brigham and Women’s Hospital. IEEE Eng Med Biol Mag. 2006 Sep-Oct;25(5):67. PMID: 17020201.

• Zollei L, Wells W. Multi-modal Image Registration Using Dirichlet-encoded Prior Information. Proceedings of the 3rd International Workshop on Biomedical Image Registration 2006; 3(WS):34-42.

• Yang Y, Zhu L, Haker S, Tannenbaum AR, Giddens DP. Harmonic skeleton guided evaluation of stenoses in human coronary arteries. Int Conf Med Image Comput Comput Assist Interv. 2005;8(Pt 1):490-7. PMID: 16685882.

• Nain D, Haker S, Bobick A, Tannenbaum AR.Multiscale 3D shape analysis using spherical wavelets. Int Conf Med Image Comput Comput Assist Interv. 2005;8(Pt 2):459-67. PMID: 16685992.

• Zhu L, Haker S, Tannenbaum A. Mass Preserving Registration for Heart MR Images. Int Conf Med Image Comput Comput Assist Interv. 2005;8(Pt 2):147-54. PMID: 16685954.