NA-MICNational 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-MICNational Alliance for Medical Image Computing http://na-mic.org

Harvard - Psychiatry Neuroimaging Laboratory

Marek Kubicki Mark DreusickeSylvain 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

National Alliance for Medical Image Computing http://na-mic.org

Update

• 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

Lateral

Males UNC Results

FemalesHarvard Results

(p=0.0027)(p=0.018)

National Alliance for Medical Image Computing http://na-mic.org

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

Automatically marked label (blue lines input by user to designate superior/dorsal point on putamen)

Post Putamen

Pre CaudatePost Caudate

Nucleus AccumbensPre Putamen

Anterior/Superior View

of Delineated Striatum

[Ramsey Al-Hakim (GaTech), James Levitt (PNL)]

National Alliance for Medical Image Computing http://na-mic.org

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.• Participants:

MIT/LMI: Lauren O’Donnell, 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

National Alliance for Medical Image Computing http://na-mic.org

Fiber Clustering: Application to NAMIC Data

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)].

Clustering algorithm: Takes traced fibers (left), extracts features from these fibers (middle), and produces a segmentation based on the similarity (right).

National Alliance for Medical Image Computing http://na-mic.org

Population Clustering

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

[O’Donnell, et al., MIT]

Cingulum Bundles Uncinate Fasciculi Corpus Callosum

National Alliance for Medical Image Computing http://na-mic.org

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

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: Sonia Pujol, Randy GollubPNL: 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. Springer-Verlag 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

[http://pnl.bwh.harvard.edu]