BIRN Publications - Research Papers


2008

Friedman, L., Turner, J.A., Stern, H., Mathalon, D.H., Trondsen, L.C., Potkin, S.G. (2008). Chronic Smoking and the BOLD Response to a Breath Hold Task in Patients with Schizophrenia and Healthy Controls. Neuroimage, 40, 1181-1194.

Keator, D.B.; Grethe, J.S.; Marcus, D.; Ozyurt, B.; Gadde, S.; Murphy, S.; Pieper, S.; Greve, D.;Notestine, R.; Bockholt, H.J.; Papadopoulos, P.; Function BIRN; Morphometry BIRN; BIRN Coordinating Center. (2008) A National Human Neuroimaging Collaboratory Enabled By The Biomedical Informatics Research Network (BIRN). IEEE Transactions on Information Technology in Biomedicine, Special Bio-Grid edition, 12 (2), 162-172.

Kim D, Manoach D, Turner J, Andreasen N, Belger A, Bockholt J, Brown G, Clark VP, Ford J, Gollub R, Lauriello J, Mathalon D, Potkin S, White T, Wible C, Calhoun VD. (2008). Analysis of the fMRI Multisite Function BIRN and MIND studies shows a unique pattern in the modulation of functional networks related to working memory in schizophrenia. Manuscript under Review.

Kim S., Smyth P., Stern H. (2008) A non-parametric Bayesian approach to modeling spatial activations in multi-site fMRI data. Manuscript under review.

Ou, W., Wells, W.M., Golland, P., (2008) Improved fMRI Detection via Combining Spatial Regularization and Anatomical Priors. Manuscript under review.

Ozyurt, I. Burak and Brown, Gregory G. Knowledge Discovery via Machine Learning for Neuro-degenerative Disease Researchers, book chapter to appear in Human Press Methods in Molecular Medicine Series Biomedical Informatics.

Potkin, S.G., Turner, J.A., Fallon, J.A., Keator, D.B., Guffanti, G., Macciardi, F., FBIRN. (2008). Gene Discovery Through Imaging Genetics - Identification of Two Novel Genes Associated with Schizophrenia. Manuscript under review.

Thomason ME; Glover GH. Controlled inspiration depth reduces variance in breath-holding induced BOLD signal. NeuroImage 39(1):206-14 (2008).

Tura, E., Turner, J.A., Fallon, J.A., Potkin, S.G. (2008). Multivariate analyses suggest genetic impacts on neurocircuitry in schizophrenia. Neuroreport, in press.

2007

Badea A, Ali-Sharief AA and Johnson GA (2007) Morphometric analysis of the C57BL/6J mouse brain. Neuroimage.

Badea A, Nicholls PJ, Johnson GA and Wetsel WC (2007) Neuroanatomical phenotypes in the reeler mouse. Neuroimage 34(4):1363-1374.

Bencheikh-Latmani R, Obraztsova A, Mackey MR, Ellisman MH and Tebo BM (2007) Toxicity of Cr(lll) to Shewanella sp. strain MR-4 during Cr(VI) reduction. Environ Sci Technol 41(1):214-220.

Bischoff-Grethe A, Ozyurt IB, Busa E, Quinn BT, Fennema-Notestine C, Clark CP, Morris S, Bondi MW, Jernigan TL, Dale AM, Brown GG and Fischl B (2007) A technique for the deidentification of structural brain MR images. Hum Brain Mapp.

Brown, G.G., Clark, C. and Liu, T.T. (2007). Measurement of cerebral perfusion with arterial spin labeling: Part 2. Applications. Journal of the International Neuropsychological Society, 13, 526-538.

Brown, G.G., Perthen, J.E., Liu, T.T., and Buxton, R.B. (2007). A primer on functional magnetic resonance imaging. Neuropsychology Review, Jun;17(2):107-25.

Bug W, Gustafson C, Shahar A, Gefen S, Fan Y, Bertrand L and Nissanov J (2007) Brain spatial normalization: indexing neuroanatomical databases, in Neuroinformatics (Crasto CJ ed), Humana Press, Totowa, NJ.

Chen, B, Song, AW, DTI Fiber Tracking with Local Tissue Property Sensitivity: Phantom and In Vivo Validation, Magn. Reson. Imag., 2007 (in press).

Chin MH, Geng AB, Khan AH, Qian WJ, Petyuk VA, Boline J, Levy S, Toga AW, Smith RD, Leahy RM and Smith DJ (2007) A genome-scale map of expression for a mouse brain section obtained using voxelation. Physiol Genomics.

Deerinck TJ, Giepmans BN, Smarr BL, Martone ME and Ellisman MH (2007) Light and electron microscopic localization of multiple proteins using quantum dots. Methods Mol Biol 374:43-54.

Eyler LT, Olsen RK, Nayak GV, Mirzakhanian H, Brown GG and Jeste DV (2007) Brain response correlates of decisional capacity in schizophrenia: a preliminary FMRI study. J Neuropsychiatry Clin Neurosci 19(2):137-144.

Farrell, JAD, Landman, BA, Jones, CK, Smith, SA, Prince, JL, van Zijl, PCM, Mori, S. Effect of SNR on the accuracy and reproducibility of DTI-derived fractional anisotropy, mean diffusivity, and principal eigenvector measurements at 1.5T, J. Magn. Reson. Imag., 2007 (in press).

Friedman, L., Stern, H., Brown, G.G., Mathalon, D., Turner, J.A., Glover, G.H., Gollub, R.L., Lauriello, J., Lim, K.O., Cannon, T., Greve, D.N., Bockholt, H.J., Belger, A., Mueller, B., Doty, M.J., He, J., Wells, W., Smyth, P.J., Pieper, S., Kim, S., Kubicki, M., Morris, S., Vangel, M., Potkin, S.G. (2007). Test-Retest and Between-Site Reliability in a Multicenter fMRI Study. Hum Brain Mapp. 2007 Jul 17; [Epub ahead of print]

Gustafson C, Bug WJ and Nissanov J (2007) NeuroTerrain--a client-server system for browsing 3D biomedical image data sets. BMC Bioinformatics 8:40.

Han X, Fischl B., Atlas renormalization for improved brain MR image segmentation across scanner platforms. IEEE Trans Med Imaging. 2007 Apr;26(4):479-86.

Johnson GA, Ali-Sharief A, Badea A, Brandenburg J, Cofer G, Fubara B, Gewalt S, Hedlund LW and Upchurch L (2007) High-throughput morphologic phenotyping of the mouse brain with magnetic resonance histology. Neuroimage.

Kim, S. and P. Smyth, Hierarchical Dirichlet processes with random effects,in Advances in Neural Information Processing Systems 19, B. Scholkopf, J. Platt, T. Hoffman (eds.), MIT Press: Cambridge, MA, 2007, pp.697-704.

Landman BA, Farrell JAD, Jones CK, Smith SA, Prince JL, Mori S. Effects of diffusion weighting schemes on the reproducibility of DTI-derived fractional anisotropy, mean diffusivity, and principal eigenvector measurements at 1.5T, NeuroImage, 36, 1123-1138 (2007).

Lin AW, Peltier ST, Grethe JS and Ellisman MH (2007) Case studies on the use of workflow technologies for scientific analysis, in Workflows for e-Science: Scientific Workflows for Grids (Taylor IJ, Deelman E, Gannon DB and Shields MS eds) p 530, Springer Publishing, New York.

Liu, T.T., and Brown, G.G. (2007). Measurement of cerebral perfusion with arterial spin labeling: Part 1. Methods. Journal of the International Neuropsychological Society, 13, 517-525.

MacKenzie-Graham A, Boline J and Toga AW (2007) Brain atlases and neuroanatomic imaging, in Neuroinformatics (Crasto CJ ed), Humana Press, Totowa, NJ.

Marcus DS, Olsen TR, Ramaratnam M and Buckner RL (2007) The extensible neuroimaging archive toolkit: an informatics platform for managing, exploring, and sharing neuroimaging data. Neuroinformatics 5(1):11-34.

Martone ME, Sargis J, Tran J, Wong WW, Jiles H and Mangir C (2007) Database resources for cellular electron microscopy. Methods Cell Biol 79:799-822.

Ngo T, Westin C-F, Golland P, A White Matter Stochastic Tractography System. 2007 MICCAI Open Science Workshop.

Ozyurt I. B. and Brown G. G., Online Meta-Search Result Refinement Via Machine Learning from Labeled-Unlabeled Data, Int. J. IT&IC vol.2 no.1, 2007 (Invited full paper from CIDM2007 conference appeared in  International Journal of Information Technology and Intelligent Computing).

Petrovic, V., Fallon, J., and Kuester, F. (2007). Visualizing whole-brain DTI tractography with gpu-based tuboids and LOD management. IEEE Transactions on Visualization and Computer Graphics (TVCG), Nov-Dec;13(6):1488-95.

Pohl KM, Kikinis R, Wells WM., Active mean fields: solving the mean field approximation in the level set framework. Inf Process Med Imaging. 2007;20:26-37.

Ruttenberg A, Clark T, Bug W, Samwald M, Bodenreider O, Chen H, Doherty D, Forsberg K, Gao Y, Kashyap V, Kinoshita J, Luciano J, Marshall MS, Ogbuji C, Rees J, Stephens S, Wong GT, Wu E, Zaccagnini D, Hongsermeier T, Neumann E, Herman I and Cheung KH (2007) Advancing translational research with the Semantic Web. BMC Bioinformatics 8 Suppl 3:S2.

Thomason ME, Foland LC and Glover GH (2007) Calibration of BOLD fMRI using breath holding reduces group variance during a cognitive task. Hum Brain Mapping 28(1):59-68.

Turner, J.A., Potkin, S.G., Brown, G.G., Keator, D.B., McCarthy, G., Glover, G.H. (2007). Neuroimaging for the diagnosis and study of mental disorders. IEEE Signal Processing Magazine, 24(4), 112-11.

Wakana S, Caprihan A., Panzenboeck MM, Fallon JH, Perry M, Gollub RL, Hua K, Zhang J, Dubey P, Blitz A, van Zijl PCM, Mori S. Reproducibility of quantitative tractography methods applied to cerebral white matter, NeuroImage, 36, 630-644 (2007).

2006

Brown, GG and Eyler, LT. (2006) Methodological and conceptual issues in functional magnetic resonance imaging: Applications to schizophrenia research. Annual Review of Clinical Psychology, Vol. 2: 51-81.

Chen B, Guo H and Song AW (2006) Correction for direction-dependent distortions in diffusion tensor imaging using matched magnetic field maps. Neuroimage 30(1):121-129.

Fennema-Notestine C, Ozyurt IB, Clark CP, Morris S, Bischoff-Grethe A, Bondi MW, Jernigan TL, Fischl B, Segonne F, Shattuck DW, Leahy RM, Rex DE, Toga AW, Zou KH and Brown GG (2006) Quantitative evaluation of automated skull-stripping methods applied to contemporary and legacy images: effects of diagnosis, bias correction, and slice location. Hum Brain Mapp 27(2):99-113.

Frey TG, Perkins GA and Ellisman MH (2006) Electron tomography of membrane-bound cellular organelles. Annu Rev Biophys Biomol Struct 35:199-224.

Friedman L and Glover GH (2006) Reducing interscanner variability of activation in a multicenter fMRI study: controlling for signal-to-fluctuation-noise-ratio (SFNR) differences. Neuroimage 33(2):471-481.

Friedman L and Glover GH (2006) Report on a multicenter fMRI quality assurance protocol. J Magn Reson Imaging 23(6):827-839.

Friedman L, Glover GH, Krenz D and Magnotta V (2006) Reducing inter-scanner variability of activation in a multicenter fMRI study: role of smoothness equalization. Neuroimage 32(4):1656-1668.

Han X, Jovicich J, Salat D, van der Kouwe A, Quinn B, Czanner S, Busa E, Pacheco J, Albert M, Killiany R, Maguire P, Rosas D, Makris N, Dale A, Dickerson B and Fischl B (2006) Reliability of MRI-derived measurements of human cerebral cortical thickness: the effects of field strength, scanner upgrade and manufacturer. Neuroimage 32(1):180-194.

Jovicich J, Czanner S, Greve D, Haley E, van der Kouwe A, Gollub R, Kennedy D, Schmitt F, Brown G, Macfall J, Fischl B and Dale A (2006) Reliability in multi-site structural MRI studies: effects of gradient non-linearity correction on phantom and human data. Neuroimage 30(2):436-443.

Keator DB, Gadde S, Grethe JS, Taylor DV and Potkin SG (2006) A general XML schema and SPM toolbox for storage of neuro-imaging results and anatomical labels. Neuroinformatics 4(2):199-212.

Kempermann G, Chesler EJ, Lu L, Williams RW and Gage FH (2006) Natural variation and genetic covariance in adult hippocampal neurogenesis. Proc Natl Acad Sci U S A 103(3):780-785.

Kim, S, Smyth, P, Stern, H. (2006).  A nonparametric Bayesian approach to detecting spatial activation patterns in fMRI data. Proceedings of the 9th International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI), October 2006.

Lee, C. P., Dourish, P., and Mark, G. 2006. The human infrastructure of cyberinfrastructure. In:  Proceedings of the 2006 20th Anniversary Conference on Computer Supported Cooperative Work (Banff, Alberta, Canada, November 04 - 08, 2006). CSCW '06. ACM Press, New York, NY, p. 483-492. 

MacFall JR, Taylor WD, Rex DE, Pieper S, Payne ME, McQuoid DR, Steffens DC, Kikinis R, Toga AW and Krishnan KR (2006) Lobar distribution of lesion volumes in late-life depression: the Biomedical Informatics Research Network (BIRN). Neuropsychopharmacology 31(7):1500-1507.

MacKenzie-Graham A, Tinsley MR, Shah KP, Aguilar C, Strickland LV, Boline J, Martin M, Morales L, Shattuck DW, Jacobs RE, Voskuhl RR and Toga AW (2006) Cerebellar cortical atrophy in experimental autoimmune encephalomyelitis. Neuroimage 32(3):1016-1023.

Magnotta VA and Friedman L (2006) Measurement of Signal-to-Noise and Contrast-to-Noise in the fBIRN Multicenter Imaging Study. J Digit Imaging 19(2):140-147.

Murphy SN, Mendis ME, Grethe JS, Gollub RL, Kennedy D and Rosen BR (2006) A web portal that enables collaborative use of advanced medical image processing and informatics tools through the Biomedical Informatics Research Network (BIRN). AMIA Annu Symp Proc :579-583.

Price DL, Chow SK, Maclean NA, Hakozaki H, Peltier S, Martone ME and Ellisman MH (2006) High-resolution large-scale mosaic imaging using multiphoton microscopy to characterize transgenic mouse models of human neurological disorders. Neuroinformatics 4(1):65-80.

Sharief AA and Johnson GA (2006) Enhanced T2 contrast for MR histology of the mouse brain. Magn Reson Med 56(4):717-725.

Turner JA, Smyth P, Macciardi F, Fallon JH, Kennedy JL and Potkin SG (2006) Imaging phenotypes and genotypes in schizophrenia. Neuroinformatics 4(1):21-49.

van der Kouwe AJ, Benner T and Dale AM (2006) Real-time rigid body motion correction and shimming using cloverleaf navigators. Magn Reson Med 56(5):1019-1032.

Williams RW (2006) Animal models in biomedical research: ethics, challenges, and opportunities, in Principles of molecular medicine (Runge MS and Patterson C eds) p 1304, Humana Press, Totowa, N.J.

2005

Ali AA, Dale AM, Badea A and Johnson GA (2005) Automated segmentation of neuroanatomical structures in multispectral MR microscopy of the mouse brain. Neuroimage 27(2):425-435.

Astakhov V, Gupta A, Santini S and Grethe JS (2005) Data Integration in the Biomedical Informatics Research Network (BIRN), in Second International Workshop, Data Integration in Life Sciences (B.Ludäscher aLR ed) p 317, Springer, San Diego, CA, USA.

Beg MF, Buckner R, Fischl B, Park Y, Ceyhan E, Priebe C, Ceritoglu C, Kolasny A, Brown T, Quinn B, Yu P, Gold B, Ratnanather JT, Miller M and BIRN BM (2005) Pattern classification of hippocampal shape analysis in a study of Alzheimer's Disease, in Human Brain Mapping Conference.

Blackwell KT (2005) A new era in computational neuroscience. Neuroinformatics 3(2):163-166.

Coggan JS, Bartol TM, Esquenazi E, Stiles JR, Lamont S, Martone ME, Berg DK, Ellisman MH and Sejnowski TJ (2005) Evidence for ectopic neurotransmission at a neuronal synapse. Science 309(5733):446-451.

Cosman ER and Wells WM, 3rd (2005) Bayesian population modeling of effective connectivity. Inf Process Med Imaging 19:39-51.

Cyr M, Caron MG, Johnson GA and Laakso A (2005) Magnetic resonance imaging at microscopic resolution reveals subtle morphological changes in a mouse model of dopaminergic hyperfunction. Neuroimage 26(1):83-90.

De Jaco A, Kovarik Z, Comoletti D, Jennings LL, Gaietta G, Ellisman MH and Taylor P (2005) A single mutation near the C-terminus in alpha/beta hydrolase fold protein family causes a defect in protein processing. Chem Biol Interact 157-158:371-372.

Deutsch A, Ludäscher B and Nash A (2005) Rewriting Queries Using Views with Access Patterns Under Integrity Constraints, in Intl Conference on Database Theory (ICDT), Edinburgh, Scotland.

Fennema-Notestine C, Ozyurt IB, Clark CP, Morris S, Bischoff-Grethe A, Bondi MW, Brown GG, Jernigan TL, Fischl B, Segonne F, Shattuck DW, Leahy RM, Rex DE, Toga AW, Zou KH and BIRN BM (2005) "Quantitative Evaluation of Automated Skull-Stripping Methods Applied to Contemporary and Legacy Images: Effects of Diagnosis, Bias Correction and Slice Selection." in Human Brain Mapping.

Grethe JS, Baru C, Gupta A, James M, Ludaescher B, Martone ME, Papadopoulos PM, Peltier ST, Rajasekar A, Santini S, Zaslavsky IN and Ellisman MH (2005) Biomedical informatics research network: building a national collaboratory to hasten the derivation of new understanding and treatment of disease. Stud Health Technol Inform 112:100-109.

Han X, Jovicich J, Salat D, van der Kouwe A, Dickerson B, Rosas D, Makris N, Dale A and Fischl B (2005) CNR Comparison of three pulse sequences for structural MR Brain Imaging, in Human Brain Mapping Conference.

Jovicich J, Czanner S, Greve D, Pacheco J, Busa E, van der Kouwe A, M. BIRN, Fischl B (2005) Test retest reproducibility assessments for longitudinal studies: quantifying MRI system upgrade effects, in International Society of Magnetic Resonance in Medicine, Miami.

Jovicich J, Czanner S, Quinn B, Pacheco J, van der Kouwe A, Snyder PJ, Analoui M, Albert M, Desikan R, Killiany R, Fischl B, Dickerson B (2005) Test-retest reliability assessment for longitudinal MRI studies: An intensity-based comparison of T1-weighted protocols and field strengths., in 11th Annual Meeting of the Organization for Human Brain Mapping, Toronto.

Jovicich J, Beg MF, Pieper S, Priebe C, Miller MM, Buckner R, Rosen B and BIRN BM (2005) Biomedical Informatics Research Network: Integrating Multi-Site Neuroimaging Data Acquisition, Data Sharing and Brain Morphometric Processing, in The 18th IEEE International Symposium on Computer-Based Medical Systems.

Kim S, Smyth P, Stern H and Turner J (2005) Parametric response surface models for analysis of multi-site fMRI data. Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv 8(Pt 1):352-359.

Lee EF, Jacobs RE, Dinov I, Leow A and Toga AW (2005) Standard atlas space for C57BL/6J neonatal mouse brain. Anat Embryol (Berl) 210(4):245-263.

Lee HJ, Turner J, Potkin SG and BIRN F (2005) Calibration Method of Functional Magnetic Resonance Images, in Proceedings of the 2005 International Conference Imaging Science, Systems, and Technology: Computer Graphics (CISST'05) pp 13-19, Las Vegas, NV.

Lucic V and Baumeister W (2005) Neuroscience. Monte Carlo places strong odds on ectopic release. Science 309(5733):387-388.

Ludäscher B, Altintas I, Berkley C, Higgins D, Jaeger-Frank E, Jones M, Lee E, Tao J and Zhao YX (2005) Scientific Workflow Management and the Kepler System. Concurrency and Computation: Practice & Experience (Special Issue on Scientific Workflows).

Ludäscher B, Lin K, Bowers S, Jaeger-Frank E, Brodaric B and Baru CX (2005) Managing Scientific Data: From Data Integration to Scientific Workflows. GSA Today (Special Issue on Geoinformatics).

Neu SC, Valentino DJ and Toga AW (2005) The LONI Debabeler: a mediator for neuroimaging software. Neuroimage 24(4):1170-1179.

Quinn B, Fenstermacher E, Han X, Pacheco J, Czanner S, van der Kouwe A, Maguire P, Raunig D, Albert M, Makris N, Desikan R, Killiany R, Dickerson B, Fischl B (2005) Test-retest reliability assessment for longitudinal MRI studies: A comparison of the effects of different T1-weighted protocols, scanner platforms, and field strengths on semi-automated hippocampal volume measures, in 11th Annual Meeting of the Organization for Human Brain Mapping, Toronto.

Turner J, Potkin SG, Brown GG, Glover GH, Fallon JH, McCarthy G, Lim KO, Gollub RL, Rosen BR, Toga AW, Kikinis R, Pieper S, Dale AM, Lauriello J, O'Leary DS, Lieberman JA, Belger A, Greve DN, Friedman L, Cannon TD, Keator DB and Grethe JS (2005) Multi-center fMRI methods and design: Function birn. Schizophrenia Bulletin 31(2):437-438.

Zou KH, Greve DN, Wang M, Pieper SD, Warfield SK, White NS, Manandhar S, Brown GG, Vangel MG, Kikinis R and Wells WM, 3rd (2005) Reproducibility of functional MR imaging: preliminary results of prospective multi-institutional study performed by Biomedical Informatics Research Network. Radiology 237(3):781-789.

2004

Beg MF, Ceritoglu C, Kolasny AE, Priebe CE, Ratnanather JT, Yashinski R, Younes L, Yu P, Jovicich J, Buckner RL, Pieper S, Fischl B and Miller MI (2004) "Biomedical Informatics Research Network: Multi-site Processing pipeline for shape analysis of brain structures." in Human Brain Mapping, Budapest.

Bischoff-Grethe A, Fischl B, Ozyurt IB, Morris S, Brown GG, Fennema-Notestine C, Clark CP, Bondi MW, Jernigan TL and BIRN BM (2004) "A technique for the deidentification of sturctural brain MR images." in Human Brain Mapping, Budapest.

Cosman E, Fisher J and Wells W (2004) "Exact MAP activity detection in fMRI using a GLM with an Ising spatial prior." in Medical Image Computing and Computer-Assisted Intervention, published in Lecture Notes in Computer Science, Springer: Berlin, St. Malot, France.

Ellisman MH, Brady M, Hart D, Lin F, Miller M and Smarr L (2004) The emerging role of biogrids. Communications of the ACM 47(11):52-57.

Ellisman MH and Peltier S (2004) Medical data federation: the biomedical informatics research network, in The grid : blueprint for a new computing infrastructure (Foster I and Kesselman C eds), Morgan Kaufmann, Amsterdam ; Boston.

Fischl B, Salat DH, van der Kouwe AJ, Makris N, Segonne F, Quinn BT and Dale AM (2004) Sequence-independent segmentation of magnetic resonance images. Neuroimage 23 Suppl 1:S69-84.

Fischl B, van der Kouwe A, Destrieux C, Halgren E, Segonne F, Salat DH, Busa E, Seidman LJ, Goldstein J, Kennedy D, Caviness V, Makris N, Rosen B and Dale AM (2004) Automatically parcellating the human cerebral cortex. Cereb Cortex 14(1):11-22.

Horne NR, Bondi MW, Fennema-Notestine C, Houston WS, Brown GG, Jernigan TL, Salmon DP, Mickes LB and Fischl B (2004) "Hippocampal and Amygdalal Brain Changes in Young-Old and Very-Old with Alzheimer's Disease: Associations with Neuropsychological Functioning." in The 9th International Conference on Alzheimer's Disease and Related Disorders.

Jovicich J, Greve D, Haley E, Kennedy D, Tosa T, Gollub RL, Fischl B, Dale A, Brain Morphometry BIRN (2004) "Multi-site structural MRI studies: an evaluation of image distortions and image intensity reproducibility." in International Society of Magnetic Resonance in Medicine, Kyoto.

Jovicich J, Haley E, Greve D, Gollub R, Kennedy D, Fischl B, Dale A, Brain Morphology BIRN (2004) "Reliability in Multi-Site Structural MRI Studies: Effects of gradient nonlinearity correction on volume and displacement of brain subcortical structures." in Human Brain Mapping, Budapest.

Jovicich J, Grethe J, MacFall J, Gollub R, Pieper S and Rosen B (2004) "Distributed collaborations using neuroinformatics and information technology innovations." in RSNA, Chicago, IL.

Lee HJ, Potkin SG, Lee S (2004) "Intelligent Reconstruction Method of MR Images." in Proceedings of 2004 International Symposium on Intelligent Signal Processing and Communication Systems, Seoul, Korea.

Lee HJ, Turner JA, FIRST BIRN (2004) "Parallel reconstruction algorithms for MRIs." in Proceedings of the 3rd International Conference on Computer and Information Science (ICIS '04) pp 55-62, Los Angeles, CA.

Lee HJ, Turner JA, FIRST BIRN (2004) "Task Distribution Methods for the Reconstruction of MR Images." in Proceedings of the 5th International Conference on Parallel and Distributed Computing, Applications and Technologies pp 257-266, Singapore.

Lee HJ, Turner JA, Potkin SG (2004) "Scalable parallel reconstruction algorithm for magnetic resonance images." in Proceedings of the 2004 International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA '04), Las Vegas, NV.

Lee HJ and Potkin SG (2004) "Fine-grain parallel reconstruction algorithm for MR images." in Proceedings of the 17th International Conference on Parallel and Distributed Computing Systems (PDCS '04) pp 383-389, San Francisco, CA.

Martone ME, Gupta A and Ellisman MH (2004) E-neuroscience: challenges and triumphs in integrating distributed data from molecules to brains. Nat Neurosci 7(5):467-472.

Nash A and Ludäscher B (2004) Processing Unions of Conjunctive Queries with Negation under Limited Access Patterns., in 9th International Conference on Extending Database Technology (EDBT), Crete, Greece.

Potkin S, Brown GG, Glover GH, McCarthy G, Lim KO, Gollub R, Rosen B, Toga A, Kikinis R, Dale A, Lauriello J, O'Leary D, Lieberman J, Belger A, Greve D, Friedman L, Cannon T, Fallon J, Keator DB, Grethe JS and Turner JA (2004) Functional biomedical informatics research network: Multi-center fMRI methods. Neuropsychopharmacology 29(Suppl. 1):S221.

Rex DE, Shattuck DW, Woods RP, Narr KL, Luders E, Rehm K, Stolzner SE, Rottenberg DA and Toga AW (2004) A meta-algorithm for brain extraction in MRI. Neuroimage 23(2):625-637.

Zou KH, Greve DN, Wang M, Pieper SD, Warfield SK, White NS, Vangel MG, Kikinis R, Wells WMI and BIRN F (2004) A prospective multi-institutional study for the reproducibility of fMRI: a preliminary report from the Biomedical Informatics Research Network., in Lecture Notes in Computer Science p 3217, Berlin, Springer.

2003

Fennema-notestine C, Ozyurt IB, Brown GG, Clark CP, Morris S, Bischoff-Grethe A, Bondi MW, Jernigan TL and Human Brain Morphometry B (2003) Bias correction, pulse sequence, and neurodegeneration influence performance of automated skull - stripping methods. Society for Neuroscience Abstract Viewer and Itinerary Planner 2003:Abstract No. 863.823.

Grethe JS, Jovicich J, Martone ME, Pieper S, Brown GG, Ellisman MH, Gollub RL, BIRN BM, BIRN M, BIRN F and Center BC (2003) The biomedical informatics research network: educational and teaching resources. Society for Neuroscience Abstract Viewer and Itinerary Planner 2003:Abstract No. 23.25.

Gupta A, Ludascher B, Grethe JS and Martone ME (2003) Towards a formalization of disease-specific ontologies for neuroinformatics. Neural Netw 16(9):1277-1292.

Gupta A, Ludascher B, Martone MER, A., Ross E, Qian X, Santini S, He H and Zaslavsky I (2003) BIRN-M: A Semantic Mediator for Solving Real-World Neuroscience Problems., in Demonstration track, ACM Intl Conference on Management of Data (SIGMOD).

Jovicich J, Greve D, Haley E, Fischl B, Dale A and BIRN BM (2003) "Biomedical Informatics Research Network: Characterization and Correction of Image Distortions in Multi-Site Structural MRI". in Human Brain Mapping Conference.

Lai IS, Hoge R, Greenberg JE, Greve D, Vangel M, Poldrack R and Gollub RL (2003) "Teaching statistical analysis of fMRI data: an online resource." in Human Brain Mapping, New York.

Ludäscher B, Gupta A and E MM (2003) A Model-Based Mediator System for Scientific Data Management. Morgan Kaufmann Publishers.

Martone ME, Zhang S, Gupta A, Qian X, He H, Price DL, Wong M, Santini S and Ellisman MH (2003) The cell-centered database: a database for multiscale structural and protein localization data from light and electron microscopy. Neuroinformatics 1(4):379-395.

Potkin SG, Andreasen N, Belger A, Brown G, Ford J, Glover G, Golub R, Heckers S, Lauriello J, Lieberman J, Lim KO, McCarley R, McCarthy G, Rosen B, Toga A, Turner J and Wible C (2003) Workshop on Multi-Site Brain FMRI Imaging Studies in Schizophrenia Using the BIRN Methodology, in Cognitive Tasks and Clinical Correlates International Congress on Schizophrenia Research Annual Meeting, Denver, CO.

Potkin SG, Turner JA, Brown GG, Glover GH, Heckers S, Keator DB, Grethe JS and Workgroups FB (2003) Biomedical informatics research network: functional imaging research in schizophrenia testbed. Society for Neuroscience Abstract Viewer and Itinerary Planner :Abstract No. 428.414.

Santini S and Gupta A (2003) The Role of Internet Imaging in the Biomedical Informatics Research Network., in SPIE (Santini S and Schettini R eds), San Jose.

Shattuck D, Rex DE, Darvas F, Leahy R and Toga AW (2003) "JohnDoe: Anonymizing MRI Data for the Protection of Research Subject Confidentiality." in Human Brain Mapping, New York.

Turner JA, Potkin SG, Brown GG, Glover GH, Greve D, Keator DB, McCarthy G, Grethe JS, Wible CG, Lim K, Toga AW, Andreasen NC, O'Leary D and BIRN F (2003) Biomedical Informatics Research Network: Integrating multi-site human functional imaging acquisition and analysis, in Biomedical Information Science and Technology Initiative (BISTI) Symposium, Bethesda, MD.

Wang T, Santini S and Gupta A (2003) An Interpolated Volume Data Model., in VLDB, Berlin.

Zhang S, Price D, Qian X, Gupta A, Ellisman MH and Martone ME (2003) "A Cell Centered Database (CCDB) for Multi-Scale Microscopy Data Management." in Microscopy and Microanalysis 2003 (M&M 2003), San Antonio, Texas.

2002

Fischl B, Salat DH, Busa E, Albert M, Dieterich M, Haselgrove C, van der Kouwe A, Killiany R, Kennedy D, Klaveness S, Montillo A, Makris N, Rosen B and Dale AM (2002) Whole brain segmentation: automated labeling of neuroanatomical structures in the human brain. Neuron 33(3):341-355.

Gupta A, Ludäscher B, Martone ME, Qian X, Ross E, Tran J, Zaslavsky I. X (2002) "KIND-2: A System for Managing Alternate Models in Integrated Views", in 19th British National Conference on Databases (BNCOD), Sheffield, UK.

Gupta A, Ludäscher B and Martone ME (2002) Registering Scientific Information Sources for Semantic Mediation., in Proc 21st International Conference on Conceptual Modeling, (ER), Tampere, Finland.

Gupta A, Ludäscher B, Martone ME, Qian X, Ross E, Tran J and Zaslavsky IX (2002) A System for Managing Alternate Models in Model-based Mediation., in British Natl Conf on Databases (BNCOD), Sheffield, UK.

Ludäscher B, Altintas I and Gupta A (2002) Time to Leave the Trees: From Syntactic to Conceptual Querying of XML., in Proc Intl Workshop on XML Data Management, in conjunction with Intl Conf on Extending Database Technology, Prague, Czech Republic.

Martone ME, Gupta A, Ludäscher B, Zaslavsky I and Ellisman MH (2002) Federation of Brain Data through Knowledge-Guided Mediation. Kluwer Academic Publishers.

Martone ME, Gupta A, Wong M, Qian X, Sosinsky G, Ludascher B and Ellisman MH (2002) A cell-centered database for electron tomographic data. J Struct Biol 138(1-2):145-155.

Miller MI, Trouve A and Younes L (2002) On the metrics and euler-lagrange equations of computational anatomy. Annu Rev Biomed Eng 4:375-405.

Qian X, Ludäscher B, Martone ME and Gupta A (2002) Navigating Virtual Information Sources with Know-ME., in Intl Conference on Extending Database Technology, demonstration track, Prague, Czech Republic.

Rajasekar AK and Wan M (2002) SRB & SRB Rack - Components of a Virtual Data Grid Architecture, in Advanced Simulation Technologies Conference (ASTC02), San Diego, CA.

Santini S, Gupta A (2002) Conceptual Integration of Multiple Partial Geometric Models., in 21st International Conference on Conceptual Modeling, Tampere, Finland.

Santini S and Gupta A (2002) Principles of schema design for multimedia databases. IEEE Transactions on Multimedia.

Santini S and Gupta A (2002) GeMBASE: A Geometric Mediator for Brain Analysis with Surface Ensembles., in 28th Int'l Conference on Very Large Databases, Hong Kong, China.

2001

Fischl B, Liu A and Dale AM (2001) Automated manifold surgery: constructing geometrically accurate and topologically correct models of the human cerebral cortex. IEEE Trans Med Imaging 20(1):70-80.

Gupta A, Ludäscher B and Martone ME (2001) An Extensible Model-Based Mediator System with Domain Maps., in 17th Intl Conference on Data Engineering (ICDE), demonstration track, Heidelberg, Germany.

Ludäscher B, Gupta A and Martone ME (2001) Model-Based Mediation with Domain Maps., in 17th Intl Conference on Data Engineering (ICDE), Heidelberg, Germany.

2000

Fischl B and Dale AM (2000) Measuring the thickness of the human cerebral cortex from magnetic resonance images. Proc Natl Acad Sci U S A 97(20):11050-11055.

Gupta A, Ludäscher B and Martone ME (2000) Knowledge-Based Integration of Neuroscience Data Sources., in 12th Intl Conference on Scientific and Statistical Database Management (SSDBM), Berlin, Germany.

Ludäscher B, Gupta A and Martone ME (2000) Model-Based Information Integration in a Neuroscience Mediator System., in 26th Intl Conference on Very Large Databases (VLDB) demo track, Cairo, Egypt.

1999

Dale AM, Fischl B and Sereno MI (1999) Cortical surface-based analysis. I. Segmentation and surface reconstruction. Neuroimage 9(2):179-194.

Fischl B, Sereno MI and Dale AM (1999) Cortical surface-based analysis. II: Inflation, flattening, and a surface-based coordinate system. Neuroimage 9(2):195-207.

Fischl B, Sereno MI, Tootell RB and Dale AM (1999) High-resolution intersubject averaging and a coordinate system for the cortical surface. Hum Brain Mapp 8(4):272-284.

Mendola JD, Dale AM, Fischl B, Liu AK and Tootell RB (1999) The representation of illusory and real contours in human cortical visual areas revealed by functional magnetic resonance imaging. J Neurosci 19(19):8560-8572.



You may also wish to consult the BIRN-wide Abstracts and Presentations publication lists, as well as the Test Bed-specific publications: BIRN Coordinating Center Publications, Function BIRN Publications, Morphometry BIRN Publications, and Mouse BIRN Publications.