namic activity report
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NA-MICNational Alliance for Medical Image Computing http://na-mic.org
NAMIC Activity Report
Polina GollandCore 1, MIT
National Alliance for Medical Image Computing http://na-mic.org
Broad Overview of Activities• Registration and Segmentation
– EM segmentation– Atlas construction
• DTI– Probabilistic tractography– DTI fiber clustering
• Shape analysis– Overcomplete wavelets
on a sphere
• fMRI – Activation profiles– Spatial patterns
National Alliance for Medical Image Computing http://na-mic.org
Outline
• Tissue classification– EM segmentation module in Slicer 3
• Group-wise registration– Atlas construction in ITK – Forward compatibility with XNAT
• Tractography– Probabilistic tractography module in Slicer 3
NA-MICNational Alliance for Medical Image Computing http://na-mic.org
Tissue Classification
Kilian Pohl (MIT/BWH), Brad Davis (Kitware), Sylvain Bouix (Harvard), Mareck Kubici (Harvard), Martha Shenton (Harvard), Sandy Wells (BWH), Polina Golland (MIT)
National Alliance for Medical Image Computing http://na-mic.org
• Structure hierarchy• Registration
– Atlas-to-subject– Multimodal
Slicer 3 Module
National Alliance for Medical Image Computing http://na-mic.org
Publications
• K.M. Pohl et al. A hierarchical algorithm for MR brain image parcellation. IEEE TMI 2007.
• L. Zollei et al. The Impact of Atlas Formation Methods on Atlas-Guided Brain Segmentation, Statistical Registration. MICCAI 2007 Statistical Registration Workshop: Pair-wise and Group-wise Alignment and Atlas Formation, 2007.
• M. Nakamura et al. Neocortical gray matter volume in first episode schizophrenia and first episode affective psychosis: a cross-sectional and longitudinal MRI study. Biological Psychiatry 2007.
• Min-Seong Koo et al. Smaller neocortical gray matter and larger sulcal CSF volumes in neuroleptic-naive females with schizotypal personalitydisorder. Archives of General Psychiatry 2006.
NA-MICNational Alliance for Medical Image Computing http://na-mic.org
Group-wise Registration
Serdar Balci (MIT), Brad Davis (Kitware), Mert Sabuncu (MIT), Lilla Zollei (MGH), Sylvain Bouix (Harvard), Mareck Kubici (Harvard), Martha Shenton (Harvard), Sandy Wells (BWH), Polina Golland (MIT)
National Alliance for Medical Image Computing http://na-mic.org
ITK command-line app
• Jointly align all images– MI or Variance– Affine or BSpline
• Optimization– Stochastic sampling – Multi-resolution – Gradient descent with line search
National Alliance for Medical Image Computing http://na-mic.org
Publications • MICCAI 2007 Statistical Registration Workshop:
– S.K. Balci et al. Free-Form B-spline Deformation Model for Groupwise Registration.
– L. Zöllei et al. The Impact of Atlas Formation Methods on Atlas-Guided Brain Segmentation.
– M.R. Sabuncu, et al. Joint Registration and Clustering of Images.
• S.K. Balci, et al. Non-rigid Groupwise Registration using B-Spline Deformation Model. MICCAI 2007 Workshop on Open-Source and Open-Data.
• A. Mewes, et al. Displacement of Brain Regions in Preterm Infants with Non-Synostotic Dolichocephaly Investigated by MRI, NeuroImage 2007.
National Alliance for Medical Image Computing http://na-mic.org
Future Work
• Explore structure within populations– Representative templates– Grouping of subjects
• Preliminary study:– Oasis dataset (oasis-brains.org)– 416 subjects, 18-96 years old– run time: 5-6h on
a 16 core 128GB PC10 20 30 40 50 60 70 80 90 100
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79.5 yrs
10 20 30 40 50 60 70 80 90 1000
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68.9 yrs
10 20 30 40 50 60 70 80 90 1000
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31.2 yrs
NA-MICNational Alliance for Medical Image Computing http://na-mic.org
DTI Tractography
Tri Ngo (MIT/BWH), Mareck Kubici (Harvard), Carl-Frederick Westin (BWH), Polina Golland (MIT)
National Alliance for Medical Image Computing http://na-mic.org
Slicer 3 Module
• MCMC sampling method– Local uncertainty: DTI tensor
• ROI initialization• Stopping criteria
National Alliance for Medical Image Computing http://na-mic.org
Publications & Plans
• T.M. Ngo, et al. A White Matter Stochastic Tractography System. MICCAI 2007 Workshop on Open-Source and Open-Data.
• Collaborative clinical study with Harvard.
National Alliance for Medical Image Computing http://na-mic.org
Broad Overview of Activities• Registration and Segmentation
– EM segmentation– Atlas construction
• DTI– Probabilistic tractography– DTI fiber clustering
• Shape analysis– Overcomplete wavelets
on a sphere
• fMRI – Activation profiles– Spatial patterns
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