2012 Progress Report

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Administrative Paperwork Timeline

  • 3/14: LOI goes to subs (Sanjay/Rachana)
  • 4/06: Signed Subcontractor's Documents due back to BWH
  • 4/09: Review by Radiology Administration (Trey/Susan)
  • 4/13: Review by BWH RA
  • 4/27: Signed Facepage and budget docs due back to Katie M for page numbering (Katie)
  • 4/30: Ship it to NIH

Scientific Report Timeline

  • 4/1: wiki page setup for progress report (Ann)
  • 4/16: all sections to be completed by owners
  • 4/16: check NIH compliance of all publications in Pubmed (Katie)
  • 4/20: create final report (Ann)
  • 4/23: Update web pages with any new materials from report (Ann)
  • 4/20: create full publications list (Katie)
  • 4/22: final review (Tina, Ron)
  • 4/23: final pdf created and submitted to Rachana (Katie)

Scientific Progress Report


Compiled from the SPL PubDB using search filter for EB005149.



  1. Choi H., Kubicki M., Whitford T.J., Alvarado J.L., Terry D.P., Niznikiewicz M., McCarley R.W., Kwon J.S., Shenton M.E. Diffusion Tensor Imaging of Anterior Commissural Fibers in Patients with Schizophrenia. Schizophr Res. 2011 Aug;130(1-3):78-85. PMID: 21561738. Keywords: Schizophrenia, Diffusion tensor imaging, Anterior commissure, White matter tractography, Fractional anisotropy, Trace

  2. Cohen-Adad J., Benner T., Greve D., Kinkel R.P., Radding A., Fischl B., Rosen B.R., Mainero C. In vivo Evidence of Disseminated Subpial T2* Signal Changes in Multiple Sclerosis at 7 T: A Surface-based Analysis. Neuroimage. 2011 Jul 1;57(1):55-62. PMID: 21511042. Keywords: Multiple sclerosis, Surface-based analysis, Subpial pathology, Ultra-high field MRI, T2-weighted

  3. Fedorov A., Li X., Pohl K.M., Bouix S., Styner M., Addicott M., Wyatt C., Daunais J.B., Wells III W.M., Kikinis R. Atlas-Guided Segmentation of Vervet Monkey Brain MRI. Open Neuroimag J. 2011; 5:186–197. PMID: 22253661. PMCID: PMC3256578. Keywords: Vervet monkey, brain MRI, brain morphology, image segmentation, image registration, open source software, 3D Slicer

  4. Gadde S., Aucoin N., Grethe J.S., Keator D.B., Marcus D.S., Pieper S. XCEDE: An Extensible Schema for Biomedical Data. Neuroinformatics. 2012 Jan;10(1):19-32. PMID: 21479735. Keywords: XML, Schema, database, Biomedical technology

  5. Gao Y., Corn B., Schifter D., Tannenbaum A. Multiscale 3D shape Representation and Segmentation with Applications to Hippocampal/Caudate Extraction from Brain MRI. Med Image Anal. 2012 Feb;16(2):374-85. PMID: 22119491. PMCID: PMC3267872. Keywords: Multiscale shape representation, Shape-based segmentation

  6. Geng X., Gouttard S., Sharma A., Gu H., Styner M., Lind W., Gerig G., Gilmore J.H.. Quantitative Tract-Based White Matter Development from Birth to Age Two Years. Neuroimage. 2012 March 28. Keywords: white matter maturation, axonal myelination, early brain development, diffusion properties, DTI atlas, fiber tracking, functional regression analysis

  7. Glasser M.F., Van Essen D.C. Mapping Human Cortical Areas in vivo Based on Myelin Content as Revealed by T1- and T2-weighted MRI. J Neurosci. 2011 Aug 10;31(32):11597-616. PMID: 21832190. PMCID: PMC3167149.

  8. Hartley C.A., Fischl B., Phelps E.A. Brain Structure Correlates of Individual Differences in the Acquisition and Inhibition of Conditioned Fear. Cereb Cortex. 2011 Sep;21(9):1954-62. PMID: 21263037. PMCID: PMC3155599.

  9. Irimia A., Chambers M.C., Alger J.R., Filippou M., Prastawa M.W., Wang B., Hovda D., Gerig G., Toga A.W., Kikinis R., Vespa P.M., Van Horn J.D. Comparison of Acute and Chronic Traumatic Brain Injury using Semi-automatic Multimodal Segmentation of MR Volumes. J Neurotrauma. 2011 Nov;28(11):2287-306. PMID: 21787171. Keywords: magnetic resonance imaging, segmentation, TBI, visualization

  10. Irimia A., Chambers M.C., Torgerson C.M., Filippou M., Hovda D.A., Alger J.R., Gerig G., Toga A.W., Vespa P.M., Kikinis R., Van Horn J.D. Patient-tailored Connectomics Visualization for the Assessment of White Matter Atrophy in Traumatic Brain Injury. Front. Neur. 3:10. doi: 10.3389/fneur.2012.00010. Keywords: connectomics, traumatic brain injury, atrophy, rehabilitation, DTI

  11. Irimia A., Van Horn J.D., Halgren E. Source Cancellation Profiles of Electroencephalography and Magnetoencephalography. Neuroimage. 2012 Feb 1;59(3):2464-74. PMID: 21959078. PMCID: PMC3254784. Keywords: Electroencephalography, Magnetoencephalography, Cancellation, Neuroimaging, Modeling

  12. Irimia A., Chambers M.C., Torgerson C.M., Horn J.D.V. Circular Representation of Human Cortical Networks for Subject and Population-level Connectomic Visualization. Neuroimage. 2012 Apr 2;60(2):1340-51. PMID: 22305988. Keywords: Connectomics , DTI, MRI, Neuroimaging, Cortical network

  13. Kim I., Tannenbaum A., Tannenbaum R. Anisotropic Conductivity of Magnetic Carbon Nanotubes Embedded in Epoxy Matrices. Carbon 2011; 49:54–61.

  14. Koven N.S., Roth R.M., Garlinghouse M.A., Flashman L.A., Saykin A.J. Regional Gray Matter Correlates of Perceived Emotional Intelligence. Soc Cogn Affect Neurosci. 2011 Oct;6(5):582-90. PMID: 20934987. PMCID: PMC3190210.

  15. Kremen W.S., Panizzon M.S., Neale M.C., Fennema-Notestine C., Prom-Wormley E., Eyler L.T., Stevens A., Franz C.E., Lyons M.J., Grant M.D., Jak A.J., Jernigan T.L., Xian H., Fischl B., Thermenos H.W., Seidman L.J., Tsuang M.T., Dale A.M. Heritability of Brain Ventricle Volume: Converging Evidence from Inconsistent Results. Neurobiol Aging. 2012 Jan;33(1):1-8. PMID: 20363053. PMCID: PMC3221930. Keywords: Aging, Alzheimer's Disease, Endophenotype, Genetics, Lateral ventricles, Mild cognitive impairment, Structural MRI, Twins

  16. Lashkari D., Sridharan R., Vul E., Hsieh P-J., Kanwisher N., Golland P. Search for Patterns of Functional Specificity in the Brain: A Nonparametric Hierarchical Bayesian Model for Group fMRI Data. Neuroimage. 2012 Jan 16;59(2):1348-68. PMID: 21884803. Keywords: fMRI, Clustering, High level vision, Category selectivity

  17. Lee J., Lankton S., Tannenbaum A. Object Tracking and Target Reacquisition Based on 3-D Range Data for Moving Vehicles. IEEE Trans Image Process. 2011 Oct;20(10):2912-24. PMID: 21486717.

  18. Looi J.C.L., Macfarlane M.D., Walterfang M., Styner M., Velakoulis D., Lätt J., Van Westen D., Nilsson C. Morphometric Analysis of Subcortical Structures in Progressive Supranuclear Palsy: In vivo Evidence of Neostriatal and Mesencephalic Atrophy. Psychiatry Res. 2011 Nov 30;194(2):163-75. PMID: 21899988. PMCID: PMC3204393. Keywords: Neostriatum, Caudate, Putamen, Mesencephalon, Magnetic resonance imaging

  19. Lyall A.E., Woolson S., Wolfe H.M., Goldman B.D., Reznick J.S., Hamer R.M., Lin W., Styner M., Gerig G., Gilmore J.H. Prenatal Isolated Mild Ventriculomegaly is Associated with Persistent Ventricle Enlargement at Ages 1 and 2. Early Hum Dev. 2012 Mar 21. PMID: 22445211. Keywords: Magnetic resonance imaging, Ultrasound, Gray matter, White matter, Cognitive development

  20. Maltbie E., Bhatt K., Paniagua B., Smith R.G., Graves M.M., Mosconi M.W., Peterson S., White S., Blocher J., El-Sayed M., Hazlett H.C., Styner M.A. Asymmetric Bias in User Guided Segmentations of Brain Structures. Neuroimage. 2012 Jan 16;59(2):1315-23. PMID: 21889995. PMCID: PMC3230681. Keywords: Manual segmentation, Subcortical structures neuroimaging, Asymmetry analysis, Rater bias

  21. McGann C., Kholmovski E., Blauer J., Vijayakumar S., Haslam T., Cates J., DiBella E., Burgon N., Wilson B., Alexander A., Prastawa M., Daccarett M., Vergara G., Akoum N., Parker D., MacLeod R., Marrouche N. Dark Regions of No-reflow on Late Gadolinium Enhancement Magnetic Resonance Imaging Result in Scar Formation after Atrial Fibrillation Ablation. J Am Coll Cardiol. 2011 Jul 5;58(2):177-85. PMID: 21718914. Keywords: Ablation, Atrium, Fibrosis, Magnetic Resonance Imaging

  22. Melonakos E.D., Shenton M.E., Rathi Y., Terry D.P., Bouix S., Kubicki M. Voxel-based Morphometry (VBM) Studies in Schizophrenia-Can White Matter Changes Be Reliably Detected with VBM?. Psychiatry Res. 2011 Aug 30;193(2):65-70. PMID: 21684124. Keywords: Diffusion tensor imaging, Meta-analysis, Chronic schizophrenia, First-episode schizophrenia, Fractional anisotropy

  23. Nakhmani A., Tannenbaum A. Self-Crossing Detection and Location for Parametric Active Contours. IEEE Trans Image Process. 2012 Feb 23. PMID: 22374361.

  24. Paniagua B., Cevidanes L., Walker D., Zhu H., Guo R., Styner M. Clinical Application of SPHARM-PDM to Quantify Temporomandibular Joint Osteoarthritis. Comput Med Imaging Graph. 2011 Jul;35(5):345-52. PMID: 21185694. PMCID: PMC3083466. Keywords: projects:ShapeAnalysisFrameworkUsingSPHARMPDM, TMJ-OA, SPHARM-PDM, Bone tissue reabsorption simulation, Bone tissue reabsorption measurement

  25. Paniagua B., Cevidanes L., Zhu H., Styner M. Outcome Quantification using SPHARM-PDM Toolbox in Orthognathic Surgery. Int J Comput Assist Radiol Surg. 2011 Sep;6(5):617-26. PMID: 21161693. PMCID: PMC3088776. Keywords: Projects:ShapeAnalysisFrameworkUsingSPHARMPDM, Orthognathic surgery, Surgical outcome, SPHARM-PDM, Statistical shape analysis

  26. Rosenberger G., Nestor P.G., Oh J.S., Levitt J.J., Kindleman G., Bouix S., Fitzsimmons J., Niznikiewicz M., Westin C-F., Kikinis R., McCarley R.W., Shenton M.E., Kubicki M. Anterior Limb of the Internal Capsule in Schizophrenia: a Diffusion Tensor Tractography Study. Brain Imaging Behav. 2012 Mar 14. PMID: 22415192. Keywords: Schizophrenia, Disconnection, MRI, Cognitive neuropsychology

  27. Sandhu R., Dambreville S., Yezzi A., Tannenbaum A. A Non-Rigid Kernel Based Framework for 2D3D Pose Estimation and 2D Image Segmentation. IEEE Trans Pattern Anal Mach Intell. 2011 Jun;33(6):1098-115. PMID: 20733218. Keywords: Statistical Learning, Image Segmentation, 3D Pose Estimation, kernel PCA

  28. Schaer M., Cuadra M.B., Schmansky N., Fischl B., Thiran J-P., Eliez S. How to Measure Cortical Folding from MR Images: a Step-by-step Tutorial to Compute Local Gyrification Index. J Vis Exp. 2012 Jan 2;(59):e3417. PMID: 22230945.

  29. Shusharina N., Sharp G. Analytic Regularization for Landmark-based Image Registration. Phys Med Biol. 2012 Mar 21;57(6):1477-98. PMID: 22390947.

  30. Venkataraman A., Rathi Y., Kubicki M., Westin C-F., Golland P. Joint Modeling of Anatomical and Functional Connectivity for Population Studies. IEEE Trans Med Imaging. 2012 Feb;31(2):164-82. PMID: 21878411.

  31. Voineskos A.N., Rajji T.K., Lobaugh N.J., Miranda D., Shenton M.E., Kennedy J.L., Pollock B.G., Mulsant B.H. Age-related Decline in White Matter Tract Integrity and Cognitive Performance: A DTI Tractography and Structural Equation Modeling Study. Neurobiol Aging. 2012 Jan;33(1):21-34. PMID: 20363050. PMCID: PMC2945445. Keywords: Aging, Anisotropy, Cognition, Diffusion tensor imaging, White matter

  32. Whitford T.J., Savadjiev P., Kubicki M., O'Donnell L.J., Terry D.P., Bouix S., Westin C-F., Schneiderman J.S., Bobrow L., Rausch A.C., Niznikiewicz M., Nestor P.G., Pantelis C., Wood S.J., McCarley R.W., Shenton M.E. Fiber Geometry in the Corpus Callosum in Schizophrenia: Evidence for Transcallosal Misconnection. Schizophr Res. 2011 Oct;132(1):69-74. PMID: 21831601. PMCID: PMC3172336. Keywords: Callosal, Diffusion-Tensor Imaging, Neurodevelopment, Morphometry, White-matter, Genu

  33. Zhu H., Kong L., Li R., Styner M., Gerig G., Lin W., Gilmore J.H. FADTTS: Functional Analysis of Diffusion Tensor Tract Statistics. Neuroimage. 2011 Jun 1;56(3):1412-25. PMID: 21335092. PMCID: PMC3085665. Keywords: Confidence band, Diffusion tensor imaging, Fiber bundle, Global test statistic, Varying coefficient model

Conference Papers

  1. Dalca A., Danagoulian G., Kikinis R., Schmidt E., Golland P. Segmentation of Nerve Bundles and Ganglia in Spine MRI Using Particle Filters. Int Conf Med Image Comput Comput Assist Interv. 2011;14(Pt 3):537-45. PMID: 22003741. PMCID: PMC3232745. Keywords: nerve bundles, tracking, segmentation, particle filter, Projects:NerveSegmentation

  2. Datar M., Gur Y., Paniagua B., Styner M., Whitaker R. Geometric Correspondence for Ensembles of Nonregular Shapes. Int Conf Med Image Comput Comput Assist Interv. 2011;14(Pt 2):368-75. PMID: 21995050.

  3. Depa M., Holmvang G., Schmidt E.J., Golland P., Sabuncu M.R. Towards Efficient Label Fusion by Pre-Alignment of Training Data. Int Conf Med Image Comput Comput Assist Interv. 2011;14(WS):38-46. Workshop on Multi-Atlas Labeling and Statistical Fusion. Keywords: Image Segmentation, Groupwise Registration, Label Fusion, Projects:NonparametricSegmentation, Projects:CardiacAblation

  4. Durrleman S., Prastawa M., Gerig G., Joshi S. Optimal Data-driven Sparse Parameterization of Diffeomorphisms for Population Analysis. Inf Process Med Imaging. 2011;22:123-34. PMID: 21761651.

  5. Fishbaugh J., Durrleman S., Piven J., Gerig G. A Framework for Longitudinal Data Analysis via Shape Regression. Proceedings of SPIE 2012;8314, 83143K

  6. Fishbaugh J., Durrleman S., Gerig G. Estimation of Smooth Growth Trajectories with Controlled Acceleration from Time Series Shape Data. Int Conf Med Image Comput Comput Assist Interv. 2011;14(Pt 2):401-8. PMID: 21995054.

  7. Gouttard S., Goodlett C.B., Kubicki M., Gerig G. Measures for Validation of DTI Tractography. Proceedings of SPIE 2012;8314, 83140J

  8. Hao X., Whitaker R.T., Fletcher P.T. Adaptive Riemannian Metrics for Improved Geodesic Tracking of White Matter. Inf Process Med Imaging. 2011;22:13-24. PMID: 21761642. PMCID: PMC3250233.

  9. Karasev P., Kolesov I., Chudy K., Tannenbaum A., Muller G., Xerogeanes J. Interactive MRI Segmentation with Controlled Active Vision. IEEE Conference on Decision and Control Dec. 2011;

  10. Langs G., Lashkari D., Sweet A., Tie Y., Rigolo L., Golby A.J., Golland P. Learning an Atlas of a Cognitive Process in its Functional Geometry. Inf Process Med Imaging. 2011;22:135-46. PMID: 21761652. PMCID: PMC3222689. Keywords: Functional connectivity atlases and tumors, Projects:ConnectivityAtlas

  11. Menze B.H., Van Leemput K., Honkela A., Konukoglu E., Weber M-A., Ayache N., Golland P. A Generative Approach for Image-based Modeling of Tumor Growth. Inf Process Med Imaging. 2011;22:735-47. PMID: 21761700. PMCID: PMC3237122. Keywords: Projects:TumorModeling

  12. Nho K., Shen L., Kim S., Swaminathan S., Risacher S.L., Saykin A.J. The Effect of Reference Panels and Software Tools on Genotype Imputation. AMIA Annu Symp Proc. 2011;2011:1013-1018. PMID: 22195161. PMCID: PMC3243280.

  13. Niethammer M., Hart G.L., Pace D.F., Vespa P.M., Irimia A., Van Horn J.D., Aylward S.R. Geometric Metamorphosis. Int Conf Med Image Comput Comput Assist Interv. 2011;14(Pt 2):639-46. PMID: 21995083.

  14. Pace D.F., Niethammer M., Aylward S.R. Sliding Geometries in Deformable Image Registration. Int Conf Med Image Comput Comput Assist Interv. 2011;14(WS):141-148. Workshop on Abdominal Imaging.

  15. Peroni M., Golland P., Sharp G.C., Baroni G. Ranking of Stopping Criteria for Log Domain Diffeomorphic Demons Application in Clinical Radiation Therapy. Conf Proc IEEE Eng Med Biol Soc. 2011;2011:4884-7. PMID: 22255433.

  16. Prastawa M., Awate S.P., Gerig G. Building Spatiotemporal Anatomical Models using Joint 4-D Segmentation, Registration, and Subject-Specific Atlas Estimation. IEEE Workshop on Mathematical Methods in Biomedical Image Analysis 2012; p. 49-56.

  17. Seshamani S., Chintalapani G., Taylor R. Iterative Refinement of Point Correspondences for 3D Statistical Shape Models. Int Conf Med Image Comput Comput Assist Interv. 2011;14(Pt 2):417-25. PMID: 21995056.

  18. Tokuda J., Hata N. OpenIGTLink Protocol Version 2. Int Conf Med Image Comput Comput Assist Interv. 2011;14(WS). Workshop on Systems & Architecture for Computer Assisted Intervention. Keywords: OpenIGTLink

  19. Wang B., Prastawa M., Irimia A., Chambers M.C., Vespa P.M., Van Horn J.D., Gerig G. A Patient-specific Segmentation Framework for Longitudinal MR Images of Traumatic Brain Injury. Proceedings of SPIE 2012;8314, 831402. Keywords: Image segmentation, Atlas formation, Longitudinal analysis

  20. Wassermann D., Rathi Y., Bouix S., Kubicki M., Kikinis R., Shenton M.E., Westin C-F. White Matter Bundle Registration and Population Analysis Based on Gaussian Processes. Inf Process Med Imaging. 2011;22:320-32. PMID: 21761667. PMCID: PMC3140022. Keywords: Diffusion MRI, White Matter Fiber Tracts, Gaussian Processes, Registration

  21. Zhu P., Awate S.P., Gerber S., Whitaker R. Fast Shape-based Nearest-neighbor Search for Brain MRIs using Hierarchical Feature Matching. Int Conf Med Image Comput Comput Assist Interv. 2011;14(Pt 2):484-91. PMID: 21995064.