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

• 2012_Progress_Report_Science_Wiki_Version (This is where authors should add their content)

Dissemination

Compiled from the SPL PubDB using search filter for EB005149.

http://www.na-mic.org/publications/pages/display?search=EB005149

Publications

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.
   
   
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: XML, Schema, database, Biomedical technology
   
   
6. 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.
   
   
7. 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.
   
   
8. 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
   
   
9. 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
   
   
10. 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
    
    
11. 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.
    
    
12. 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
    
    
13. 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
    
    
14. 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.
    
    
15. 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
    
    
16. 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
    
    
17. 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
    
    
18. 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
    
    
19. 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
    
    
20. 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
    
    
21. 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
    
    
22. 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
    
    
23. 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.
    
    
24. 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.
    
    
25. 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.
    
    
26. 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.

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.
   
   
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. 2010;14(WS):38-46. Workshop on Multi-Atlas Labeling and Statistical Fusion.
   
   
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. 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.
   
   
10. 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.
    
    
11. 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.
    
    
12. 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.
    
    
13. 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.
    
    
14. 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.
    
    
15. 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.
    
    
16. 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.
    
    
17. 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.