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.
Download ReportTranscript 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 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 • • • • • 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. • 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 • • • • 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]