1. Polina Golland Core 1, MIT
NAMIC Activity Report
Polina Golland
Core 1, MIT

2. 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

3. Outline Tissue classification Group-wise registration Tractography
EM segmentation module in Slicer 3
Group-wise registration
Atlas construction in ITK
Forward compatibility with XNAT
Tractography
Probabilistic tractography module in Slicer 3

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

5. Slicer 3 Module Structure hierarchy Registration Atlas-to-subject
Multimodal

6. 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.

7. 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)

8. ITK command-line app Jointly align all images Optimization
MI or Variance
Affine or BSpline
Optimization
Stochastic sampling
Multi-resolution
Gradient descent with line search

9. 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.

10. Future Work Explore structure within populations Preliminary study:
79.5 yrs
68.9 yrs
31.2 yrs
Explore structure within populations
Representative templates
Grouping of subjects
Preliminary study:
Oasis dataset (oasis-brains.org)
416 subjects, years old
run time: 5-6h on a 16 core 128GB PC

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

12. Slicer 3 Module MCMC sampling method ROI initialization
Local uncertainty: DTI tensor
ROI initialization
Stopping criteria

13. 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.

14. 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