NAMIC Activity Report
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![Page 1: NAMIC Activity Report](https://reader031.fdocuments.in/reader031/viewer/2022020106/56813537550346895d9c9b40/html5/thumbnails/1.jpg)
NA-MICNational Alliance for Medical Image Computing http://na-mic.org
NAMIC Activity Report
Polina GollandCore 1, MIT
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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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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
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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)
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National Alliance for Medical Image Computing http://na-mic.org
• Structure hierarchy• Registration
– Atlas-to-subject– Multimodal
Slicer 3 Module
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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.
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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)
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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
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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.
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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
0
5
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79.5 yrs
10 20 30 40 50 60 70 80 90 1000
5
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68.9 yrs
10 20 30 40 50 60 70 80 90 1000
10
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31.2 yrs
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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)
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National Alliance for Medical Image Computing http://na-mic.org
Slicer 3 Module
• MCMC sampling method– Local uncertainty: DTI tensor
• ROI initialization• Stopping criteria
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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.
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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