1. http://pnl.bwh.harvard.edu http://synapse.hitchcock.org
Core 3.1 Activities Harvard - Psychiatry Neuroimaging Laboratory and Dartmouth - Brain Imaging Laboratory

2. Update Retrospective and prospective data IRB
Progress in adapting NA-MIC kit
Issues with the NA-MIC kit
Identification of tractable problems

3. Overview - Harvard Core 1 and Core 3.1 Activities

4. Core 1 and Core 3.1 Activities
University of North Carolina
Georgia Tech
Utah
MIT

5. Core 1 and Core 3.1 - UNC Shape analysis of caudate.
Automatic segmentation of corpus callosum based on diffusion fiber tracking model.
ITK SNAP: Level set semiautomatic segmentation tool.
Statistical analysis of DTI measures along fiber tracts.
Participants:
UNC: Isabelle Corouge, Martin Styner, Guido Gerig
PNL: Sylvain Bouix, Marek Kubicki, James Levitt, Marc Niethammer, Mark Dreusicke, Adam Cohen, Doug Markant, Martha Shenton

6. Shape Analysis of Caudate (raw p-values, right)
Shape Analysis of Caudate (raw p-values, right) (Schizotypal Personality Disorder)
Medial
Males
UNC Results
Females
Harvard Results
Lateral
(p=0.018)
(p=0.0027)

7. Core 1 and Core 3.1 – GTech
Semiautomatic segmentation and parcellation of basal ganglia/striatum.
Participants:
GTech: Ramsey Al-Hakim, Delphine Nain, Allen Tannenbaum
PNL: Sylvain Bouix, James Levitt, Marc Niethammer, Laura Rosow, Marek Kubicki, Martha Shenton

8. Rule Based Segmentation of the Striatum in Slicer
Post Putamen
Pre Caudate
Post Caudate
Nucleus Accumbens
Pre Putamen
Anterior/Superior View
of Delineated Striatum
Automatically marked label (blue lines input by user to designate superior/dorsal point on putamen)
[Ramsey Al-Hakim (GaTech), James Levitt (PNL)]

9. Core 1 and Core Utah
New anisotropic measures for white matter diffusion.
Participants:
UTAH: Tom Fletcher, Ross Whitaker
PNL: Sylvain Bouix, Marek Kubicki, Martha Shenton

10. EXAMPLES HERE OF NEW MEASURES-UTAH?
???? PUT IN DATA HERE FOR UTAH – or SKIP ????

11. Core 1 and Core MIT
Diffusion measures along cingulum bundle fiber tracts.
Clustering of specific fiber tracts based on location & regions they connect.
Atlas of human brain white matter fiber bundles using automatic population based clustering.
FA/Trace measures of corpus callosum and anterior commissure.
Brain tissue segmentation and subparcellation of brain structures.
Participants:
MIT/LMI: Lauren O’Donnell, Kilian Pohl, Scott Hoge, Raul San Jose, CF Westin, Sandy Wells, Eric Grimson
PNL: Sylvain Bouix, Marek Kubicki, Motiaki Nakamura, Marc Niethammer, Mark Dreusicke, Min-Seong Koo, Doug Markant, Martha Shenton

12. Fiber Clustering: Application to NAMIC Data
Clustering algorithm: Takes traced fibers (left), extracts features from these fibers (middle), and produces a segmentation based on the similarity (right).
Left and Right Fornix
Uncinate Fasciculus and Inferior
Occipito-Frontal Fasciculus
Splenium of the Corpus Callosum
[O’Donnell L, Kubicki M, Shenton, ME, Dreusicke M,
Grimson E, Westin, CF: A Method for Clustering White
Matter Fiber Tracts. Am J Neuroradiol (In Press)].

13. Population Clustering
Automatic generation of white matter fiber bundles based on shape similarity across subjects.
Cingulum Bundles
Uncinate Fasciculi
Corpus Callosum
[O’Donnell, et al., MIT]

14. Core 2 and Core 3.1 Activities
Bug reporting and tracking.
Prototype testing.
Feature requests.
Backward compatibility testing.
Participants:
Core 2/LMI: Nichole Aucoin, Katie Hayes, Alex Yarmakovich, Raul San Jose, CF Westin, Steve Pieper
PNL: Sylvain Bouix, Marc Niethammer, Katharina Quintus

15. Core 5 and Core 3.1 Activities
Contributed to training material.
Participated in training sessions both as trainer and trainee.
Hosted one-on-one advanced training sessions.
Participants:
Core 5: Sonia Pujol, Randy Gollub
PNL: Sylvain Bouix, Laura Rosow, Adam Cohen, Erin Connor, Kathleen Long

16. Workshop
Wish List.
Identification of Tractable Problems.

17. Publications Biomedical and Clinical Applications
Nakamura M, McCarley RW, Kubicki M, Dickey CC, Niznikiewicz MA, Voglmaier MM, Seidman LJ, Maier SE, Westin CF, Kikinis R, Shenton ME. Fronto-temporal disconnectivity in schizotypal personality disorder: a diffusion tensor imaging study. Biol Psychiatry Sep 15;58(6):
Koo MS, Levitt JJ, McCarley RW, Seidman LJ, Dickey CC, Niznikiewicz MA, Voglmaier MM, Zamani P, Long KL, Kim SS, Shenton ME. Reduction of caudate volume in neuroleptic-naive female subjects with schizotypal personality disorder. Biol Psychiatry (In Press).
Kuroki N, Kubicki M, Nestor PG, Salisbury DF, Park HJ, Levitt JJ, Woolston S, Frumin M, Niznikiewicz M, Westin CF, Maier SE, McCarley RW, Shenton ME. Fornix integrity and hippocampal volume in male schizophrenic patients. Biol Psychiatry (In Press).
Onitsuka T, Niznikiewicz MA, Spencer KM, Frumin M, Kuroki N, Lucia LC, Shenton ME, McCarley RW: Schizophrenia is associated with functional and structural deficits in brain regions subserving face processing. Am J Psychiatry (In Press).

18. Publications (continued)
Algorithm Development
Eric Pichon, Delphine Nain, and Marc Niethammer. A Laplace Equation Approach for Shape Comparison. Proc SPIE Medical Imaging, 2006.
K.M. Pohl, J. Fisher, J.J. Levitt, M.E. Shenton, R. Kikinis, W.E.L. Grimson, and W.M. Wells, “ A Unifying Approach to Registration, Segmentation, and Intensity Correction, ” In Proc. MICCAI 2005: Eighth International Conference on Medical Image Computing and Computer Assisted Intervention, Palm Springs, CA, USA, Springer-Verlag, Part I, vol of Lecture Notes in Computer Science, pp , 2005
K.M. Pohl, S. Bouix, M.E. Shenton, W.E.L. Grimson, R. Kikinis, “Automatic Segmentation Using Non-Rigid Registration ” In short communications of MICCAI 2005: Eighth International Conference on Medical Image Computing and Computer Assisted Intervention, Palm Springs, CA, USA, 2005
Martin-Fernandez M, Bouix S, Ungar L, McCarley RW, Shenton ME. Two Methods for Validating Brain Tissue Classifiers. MICCAI 2005, Palm Springs, CA, USA: J. Duncan and G. Gerig (Eds.): Lecture Notes in Computer Science, volume 3749, pp , Springer-Verlag Berlin Heidelberg, 2005.
O’Donnell L, Kubicki M, Shenton ME, Dreusicke MH, Grimson WEL, Westin CF. A method for clustering white matter fiber tracts. AJNR (In Press).

19. Members of the Psychiatry Neuroimaging Laboratory, Brigham and Women’s Hospital, and the Laboratory of Neuroscience, Brockton VA - HMS
PUT IN DATA HERE [