NA-MIC
National Alliance for Medical Image Computing
http://na-mic.org
Core 3.1 Activities
Harvard - Psychiatry Neuroimaging Laboratory
and
Dartmouth - Brain Imaging Laboratory
http://pnl.bwh.harvard.edu
http://synapse.hitchcock.org
NA-MIC
National Alliance for Medical Image Computing
http://na-mic.org
Harvard - Psychiatry Neuroimaging Laboratory
Marek Kubicki
Sylvain Bouix
Marc Niethammer
Katharina Quintus
Motoaki Nakamura
Doug Markant
Mark Dreusicke
Adam Cohen
Laura Rosow
James Levitt
Min-Seong Koo
Erin Connor
http://pnl.bwh.harvard.edu
Update
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Retrospective and prospective data
IRB
Progress in adapting NA-MIC kit
Issues with the NA-MIC kit
Identification of tractable problems
National Alliance for Medical Image Computing
http://na-mic.org
Overview - Harvard
• Core 1 and Core 3.1 Activities
• Core 2 and Core 3.1 Activities
• Core 5 and Core 3.1 Activities
National Alliance for Medical Image Computing
http://na-mic.org
Core 1 and Core 3.1 Activities
• University of North Carolina
• Georgia Tech
• Utah
• MIT
National Alliance for Medical Image Computing
http://na-mic.org
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
National Alliance for Medical Image Computing
http://na-mic.org
Shape Analysis of Caudate
(raw p-values, right)
(Schizotypal Personality Disorder)
Medial
Males
UNC Results
(p=0.018)
Females
Harvard Results
Lateral
National Alliance for Medical Image Computing
http://na-mic.org
(p=0.0027)
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
National Alliance for Medical Image Computing
http://na-mic.org
Rule Based Segmentation of
the Striatum in Slicer
Post Caudate
Pre Caudate
Anterior/Superior
View
of Delineated
Striatum
Post
Putamen
Pre Putamen
Nucleus
Accumbens
National Alliance for Medical Image Computing
http://na-mic.org
Automatically marked label (blue
lines input by user to designate
superior/dorsal point on putamen)
[Ramsey Al-Hakim (GaTech), James Levitt (PNL)]
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
National Alliance for Medical Image Computing
http://na-mic.org
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
National Alliance for Medical Image Computing
http://na-mic.org
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.
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Participants:
MIT/LMI:
PNL:
Lauren O’Donnell, Kilian Pohl, Scott Hoge, Raul San Jose,
CF Westin, Sandy Wells, Eric Grimson
Sylvain Bouix, Marek Kubicki, Motoiaki Nakamura, Marc
Niethammer, Mark Dreusicke, Min-Seong Koo, Doug Markant,
Martha Shenton
National Alliance for Medical Image Computing
http://na-mic.org
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
National Alliance for Medical Image Computing
http://na-mic.org
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)].
Population Clustering
Automatic generation of
white matter fiber bundles
based on shape similarity
across subjects.
Cingulum Bundles
Uncinate Fasciculi
National Alliance for Medical Image Computing
http://na-mic.org
Corpus Callosum
[O’Donnell, et al., MIT]
Core 2 and Core 3.1 Activities
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Bug reporting and tracking.
Prototype testing.
Feature requests.
Backward compatibility testing.
• Participants:
Core 2/LMI:
PNL:
Nichole Aucoin, Katie Hayes,
Alex Yarmakovich, Raul San Jose,
CF Westin, Steve Pieper
Sylvain Bouix, Marc Niethammer,
Katharina Quintus
National Alliance for Medical Image Computing
http://na-mic.org
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:
PNL:
Sonia Pujol, Randy Gollub
Sylvain Bouix, Laura Rosow, Adam
Cohen, Erin Connor, Katherine Long
National Alliance for Medical Image Computing
http://na-mic.org
Workshop
• Wish List.
• Identification of Tractable Problems.
National Alliance for Medical Image Computing
http://na-mic.org
Publications
•
Biomedical and Clinical Applications
1.
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 15;58(6):468-78.
2.
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).
3.
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).
4.
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).
National Alliance for Medical Image Computing
http://na-mic.org
Publications (continued)
•
Algorithm Development
1.
Eric Pichon, Delphine Nain, and Marc Niethammer. A Laplace Equation Approach for Shape
Comparison. Proc SPIE Medical Imaging, 2006.
2.
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
3.
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
4.
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. SpringerVerlag Berlin Heidelberg, 2005.
5.
O’Donnell L, Kubicki M, Shenton ME, Dreusicke MH, Grimson WEL, Westin CF. A
method for clustering white matter fiber tracts. AJNR (In Press).
National Alliance for Medical Image Computing
http://na-mic.org
Members of the Psychiatry Neuroimaging Laboratory,
Brigham and Women’s Hospital, and the
Laboratory of Neuroscience, Brockton VA - HMS
• PUT IN DATA HERE
National Alliance for Medical Image Computing
http://na-mic.org
[http://pnl.bwh.harvard.edu]