1. Harvard Psychiatry Neuroimaging Laboratory
Harvard Psychiatry Neuroimaging Laboratory
Site PI: Martha E. Shenton, Ph.D.
... to use computational tools to further our
understanding of brain abnormalities in schizophrenia ...

2. Researchers on Team Martha Shenton, Ph.D. Marek Kubicki, M.D., Ph.D.
Sylvain Bouix, Ph.D.
James Levitt, M.D.
Marc Niethammer, Ph.D.
Katharina Quintus, M.S.
Moto Nakamura M.D., Ph.D.
Toshiaki Onitsuka, M.D., Ph.D.
Min-Seong Koo, M.D., Ph.D.
Noriomi Kuroki, M.D., Ph.D.
Mark Dreusicke, B.A.
Doug Markant, B.A.

3. PNL Impact on NAMIC Provide Data (structural and diffusion MRI)
Diffusion Data: chronic schizophrenics (SZ) and 40 controls (LSDI, 1.5 Tesla) chronic schizophrenics and 12 controls (SENSE EPI, 3.0 Tesla) Structural Data:
14 schizotypal personality disorder, 23 SZ, 27 first episode SZ, 26
first episode affective disorder, plus matched controls and labelmaps.
Influencing tool and algorithm design based on
User feedback (e.g., algorithms, 3D slicer, user interface) Study demands (e.g., define problems needing solutions)
Applying tools and algorithms developed within NAMIC

4. Collaborations within NAMIC
UNC
Shape analysis of caudate,
Corpus Callosum subdivision.
MIT
Optimal path analysis (using fMRI activation for seeding),
Stochastic tracking,
Spectral clustering,
Segmentation (STG, amygdala/hippocampal complex).
GaTech
Semiautomatic parcellation of the striatum,
Spherical wavelets.
Utah
Smoothing of diffusion weighted images.

5. Examples of NAMIC Success Stories
Fiber Atlas and Clustering
... beyond global analysis of
diffusion properties.
Shape Analysis
... beyond volumetric
analysis.
Automatic
Segmentation
... validated, robust,
efficient.

6. Publications Biomedical/Clinical Applications
(1) Nakamura M, McCarley RW, Kubicki M, Dickey CC, Niznikiewicz MA, Voglmaier MM, Seidman LJ, Maier SE, Westin CF, Kikinis R, and Shenton ME. Fronto-temporal disconnectivity in schizotypal personality disorder: A diffusion tensor imaging study. Biol Psychiatry 2005;58(6):
(2) 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 2006;60:22-31.
(3) Onitsuta T, Niznikiewicz MA, Spencer KM, Frumin M, Kuroki N, Lucia LC, Shenton ME, McCarley RW. Functional and structural deficits in brain regions subserving face perception in schizophrenia. Am J Pschiatry 2006;163(3):
(4) 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 2006;60:40-48.

7. Publications Algorithm Development
(5) O’Donnell L, Kubicki M, Shenton ME, Dreusicke MH, Grimson WEL, Westin CF. A method for clustering white matter fiber tracts. AJNR 2006;27:
(6) Martin-Fernandez M, Bouix S, Ungar L, McCarley RW, Shenton ME. Two Methods for Validating Brain Tissue Classifiers. Eighth International Conference on Medical Image Computing and Computer Assisted Intervention, 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.
(7) Bouix S, Martin-Fernandez M, Ungar L, Shenton ME, McCarley RW. Automatic evaluation of brain MR segmentation techniques by level of agreement. In 11th Annual Meeting of the Organization for the Human Brain Mapping. Toronto, ON, Canada, 2005.
(8) Pohl KM, Bouix S, Shenton ME, Grimson WEL, Kikinis R. Automatic segmentation using non-rigid registration. In short communications of MICCAI 2005: Eighth International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Palm Springs, CA, USA, 2005.
(9) Niethammer M, Estepar RSJ, Bouix S, Shenton ME, Westin CF. On diffusion tensor estimation. In International Conference of the Engineering in Medicine and Biology Society. New York City, New York, USA: IEEE, 2006.

8. Publications Algorithm Development, cont.
(10) Pohl KM, Fisher F, Levitt JJ, Shenton ME, Kikinis R, Grimson WEL, Wells WM. A unifying approach to registration, segmentation, and intensity correction. Eighth International Conference on Medical Image Computing and Computer Assisted Intervention, 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.
(11) Pohl KM, Fisher J, Shenton M, McCarley R, Grimson WEL, Kikinis R, Wells WW. Logarithm Odds Maps for Shape Represention. Ninth International Conference on Medical Image Computing and Computer Assisted Intervention, MICCAI 2006, Lecture Notes in Computer Science, volume 4191, pp , Springer Berlin, Heidelberg 2006 ( ).
(12) Niethammer M, Bouix S, Westin C-F, Shenton M. Fiber Bundle Estimation and Parameterization. Ninth International Conference on Medical Image Computing and Computer Assisted Intervention, MICCAI 2006; 4191:
(13) Styner M, Oguz I, Xu S, Brechbuhler C, Pantazis D, Levitt J, Shenton M, Gerig G. Framework for the statistical shape analysis of brain structures using SPHARM-PDM. Open Science Workshop at the Ninth International Conference on Medical Image Computing and Computer Assisted Intervention, MICCAI 2006, Copenhagen, published at Insight Journal Dspace link:

9. Projects/Papers Submitted or About To Be Submitted
Biomedical/Clinical Applications:
UF: 2 R01 tractography analysis with mean FA measures, doDTI, submitted to Brain. (#14)
CF: Previously defined ROIs, tractography with behavior Stroop data, doDTI, submitted to Archives General Psychiatry. (#15)
STG: STG automatic segmentation (MIT) – submitted to NeuroImage. (#16)
STG: Mean FA, mean diffusivity within ROI defined on SPGR, Slicer, ready to be submitted – Biological Psychiatry. (#17)
Ca: Caudate shape analysis (UNC) – ready to be submitted to Biological Psychiatry. (#18)

10. Projects/Papers Submitted or About To Be Submitted
Algorithm Development:
Bouix S, Martin-Fernandex M, Ungar L, Nakamura M, Koo MS, McCarley RW, Shenton ME. On evaluating brain tissue classifiers without a ground truth. Submitted to Neuroimage. (#19)
Pohl KM, Bouix S, Nakamura M, Rohlfing T, McCarley RW, Kikinis R, Grimson WEL, Shenton ME, Wells WM. A heirarchical algorithm for MR brain image parcellation. Submitted to IEEE Transactions on Medical Imaging. (#20)
Pohl KM, Fisher J, Bouix S, Grimson WEL, Kikinis R, Wells WM. Using the logarithm of odds to define a vector space on probabilistic atlases. Submitted to Medical Image Analysis. (#21)

11. NAMIC Impact on the PNL
Improved processing pipeline (e.g., one-click segmentation).
Advanced analysis of structural data (e.g., shape analysis with spherical harmonics/spherical wavelets; improved statistics).
Advanced analysis of diffusion data (e.g., new tractography methods, clustering and evaluation of tractography results, easier workflow through standardized diffusion format (NRRD)).