Core 3.1 Activities Harvard Psychiatry Neuroimaging Laboratory and Dartmouth Brain Imaging Laborator

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Core 3.1 Activities Harvard -
Psychiatry Neuroimaging Laboratory
and Dartmouth - Brain Imaging Laboratory

• http//pnl.bwh.harvard.edu
• http//synapse.hitchcock.org

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Harvard - Psychiatry Neuroimaging
Laboratory Marek Kubicki Mark
Dreusicke Sylvain Bouix Adam
Cohen Marc Niethammer Laura Rosow
Katharina Quintus James Levitt
Motoaki Nakamura Min-Seong Koo Doug
Markant Erin Connor

• http//pnl.bwh.harvard.edu

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Update

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

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Overview - Harvard

• Core 1 and Core 3.1 Activities
• Core 2 and Core 3.1 Activities
• Core 5 and Core 3.1 Activities

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Core 1 and Core 3.1 Activities

• University of North Carolina
• Georgia Tech
• Utah
• MIT

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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

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Shape Analysis of Caudate(raw p-values,
right) (Schizotypal Personality Disorder)
Medial
Males UNC Results
Females Harvard Results
Lateral
(p0.0027)
(p0.018)
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Core 1 and Core 3.1 GaTech

• Semiautomatic segmentation and parcellation of
  basal ganglia/striatum.
• Participants
• GaTech Ramsey Al-Hakim, Delphine Nain,
  Allen Tannenbaum
• PNL Sylvain Bouix, James Levitt,
  Marc Niethammer,
  Laura Rosow, Marek
  Kubicki, Martha Shenton

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Rule Based Segmentation of the Striatum in Slicer
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)
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Core 1 and Core 3.1 - Utah

• New anisotropy measures for white matter
  diffusion.
• Hypothesis tests for DTI using full tensor
  information.
• Anisotropic filtering of DTI.
• Participants
• UTAH Tom Fletcher, Saurav Basu, Ross
  Whitaker
• PNL Sylvain Bouix, Marek Kubicki,
  Martha Shenton

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Preliminary Results - Utah

• Hypothesis Testing
• Synthetic examples show higher statistical power
  of full-tensor tests over FA tests.
• Applied to cingulum bundle data (schizophrenia
  and control groups).
• Similar results (p-values) to those using FA --
  more tests needed.
• Filtering

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Core 1 and Core 3.1 - 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 ODonnell, Kilian Pohl,
  Scott Hoge, Raul San Jose, CF Westin, Sandy
  Wells, Eric Grimson
• PNL Sylvain Bouix, Marek Kubicki,
  Motoiaki Nakamura, Marc Niethammer, Mark
  Dreusicke, Min-Seong Koo, Doug Markant, Martha
  Shenton

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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).
Uncinate Fasciculus and Inferior
Occipito-Frontal Fasciculus
Splenium of the Corpus Callosum
Left and Right Fornix
ODonnell L, Kubicki M, Shenton,
ME, Dreusicke M, Grimson E,
Westin, CF A Method for Clustering White
Matter Fiber Tracts. Am J Neuroradiol
(In Press).
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Population Clustering

• Automatic generation of white matter fiber
  bundles based on shape similarity across subjects.

Cingulum Bundles
Uncinate Fasciculi
Corpus Callosum
ODonnell, et al., MIT
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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
  

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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, Katherine Long

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Workshop

• Wish List.
• Identification of Tractable Problems.

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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. 2005 Sep 1558(6)468-78.
  
• 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).

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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. 3749 of Lecture Notes in Computer Science,
  pp. 310-318, 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
  515-522, 2005. Springer-Verlag Berlin Heidelberg,
  2005.
• ODonnell L, Kubicki M, Shenton ME, Dreusicke MH,
  Grimson WEL, Westin CF. A method for clustering
  white matter fiber tracts. AJNR (In Press).

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Members of the Psychiatry Neuroimaging
Laboratory, Brigham and Womens Hospital, and
the Laboratory of Neuroscience, Brockton VA - HMS

• PUT IN DATA HERE

http//pnl.bwh.harvard.edu