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

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.
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.
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.
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.
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.
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
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.
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.
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.
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.
16. 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.
17. 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.
18. 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.
19. 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.
20. 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.
21. 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.
22. 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.
23. 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.
24. 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.
25. 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. 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. 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. 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., Gerig G. Estimation of Smooth Growth Trajectories with Controlled Acceleration from Time Series Shape Data. Med Image Comput Comput Assist Interv. 2011;14(Pt 2):401-8. PMID: 21995054.
6. 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.
7. 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.
8. 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.
9. 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.
10. Niethammer M., Hart G.L., Pace D.F., Vespa P.M., Irimia A., Van Horn J.D., Aylward S.R. Geometric Metamorphosis. Med Image Comput Comput Assist Interv. 2011;14(Pt 2):639-46. PMID: 21995083.
11. Seshamani S., Chintalapani G., Taylor R. Iterative Refinement of Point Correspondences for 3D Statistical Shape Models. Med Image Comput Comput Assist Interv. 2011;14(Pt 2):417-25. PMID: 21995056.
12. Tokuda J., Hata N. OpenIGTLink Protocol Version 2. Med Image Comput Comput Assist Interv. 2011;14(WS). Workshop on Systems & Architecture for Computer Assisted Intervention
13. 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.
14. Zhu P., Awate S.P., Gerber S., Whitaker R. Fast Shape-based Nearest-neighbor Search for Brain MRIs using Hierarchical Feature Matching. Med Image Comput Comput Assist Interv. 2011;14(Pt 2):484-91. PMID: 21995064.