NAMIC Activity Report

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


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


Tissue Classification

Kilian Pohl (MIT/BWH), Brad Davis (Kitware), Sylvain Bouix (Harvard), Mareck Kubici (Harvard), Martha Shenton (Harvard), Sandy Wells (BWH), Polina Golland (MIT)


• Structure hierarchy• Registration

– Atlas-to-subject– Multimodal

Slicer 3 Module


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.


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)


ITK command-line app

• Jointly align all images– MI or Variance– Affine or BSpline

• Optimization– Stochastic sampling – Multi-resolution – Gradient descent with line search


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.


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


DTI Tractography

Tri Ngo (MIT/BWH), Mareck Kubici (Harvard), Carl-Frederick Westin (BWH), Polina Golland (MIT)


Slicer 3 Module

• MCMC sampling method– Local uncertainty: DTI tensor

• ROI initialization• Stopping criteria


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.


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

Documents

NAMIC Activity Report