2006

Bischoff-Grethe A., Fennema-Notestine C., Kaelberer M., Brown G.G., and Fischl B. The anonymization of cranial MR images: A behavioral study. Society for Neuroscience Annual Meeting (2006).

Chiang MC, Dutton RA, Hayashi KM, Toga AW, Lopez OL, Aizenstein HJ, Becker JT, Thompson PM (2006). Fluid Registration of Medical Images using Jensen-Renyi Divergence Reveals 3D Profile of Brain Atrophy in HIV/AIDS, IEEE International Symposium on Biomedical Imaging (ISBI2006), April 6-9 2006.

Chiang MC, Dutton RA, Hayashi KM, Toga AW, Lopez OL, Aizenstein HJ, Becker JT, Thompson PM. 3D Pattern of Brain Atrophy in HIV/AIDS Mapped using Tensor-Based Morphometry, Annual Meeting of the American Academy of Neurology, 2006.

Estepar, R. San Jose, M. Kubicki, M. Sentón, C-F Westin, A Kernel-based Approach for User-guided Fiber Bundling using Difusion Tensor Data, IEEE 2006 Int. Conf. of the Engineering in Medicine and Biology Society, 2006.

Fennema-Notestine, C. Morphometry BIRN: Structural MRI provides a myriad of information to advance our understanding of neurodegenerative disease. Presented in Plenary Session Technological Advances in Neuroimaging Translate into Deeper Understanding of Brain Structure and Function: A Joint Presentation of the Biomedical Informatics Research Network (BIRN) Testbeds, Spring Brain Conference, Sedona, AZ, 2006.

Gupta A., C. Bean, W. Bug, C. Fennema-Notestine, M. E. Martone, J. A. Turner, J. S. Grethe. Creating a community-based knowledge management framework for integrating neuroscience data via ontologies. Society for Neuroscience Annual Meeting (2006).

Keator, D.B., Ozyurt, B., Wei, D., Gadde, S., Potkin, S.G., Brown, G., Morphometry BIRN, FBIRN., Grethe, J. (2006). A General and Extensible Multi-Site Database and XML based Informatics System for the Storage, Retrieval, Transport and Maintenance of Human Brain Imaging and Clinical Data. Annual Meeting of the Organization for Human Brain Mapping, Florence, Italy, June 11-15, 2006.

Kindlmann G., Xavier Tricoche, C.-F. Westin, Anisotropy Creases Delineate White Matter Structure in Diffusion Tensor MRI, Ninth International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI'06). October, 2006. http://lmi.bwh.harvard.edu/papers/papers/kindlmannMICCAI06.html

Kolasny A , MF Beg, C Ceritoglu, T Brown, Y Park, C Priebe, M Miller, B Fishl, R Buckner (2006) BIRN and Computational Anatomy: A TeraGrid Technology, a poster presented at the first annual TeraGrid Conference, 12-June-2006, Indianapolis, Indiana.

O'Donnell Lauren and Carl-Fredrik Westin, High-Dimensional White Matter Atlas Generation and Group Analysis, Ninth International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI'06). October, 2006.

O'Donnell Lauren , Carl-Fredrik Westin, A High-Dimensional Fiber Tract Atlas, 14th Annual International Society of Magnetic Resonance in Medicine (ISMRM) Seattle, Washington (2006). http://people.csail.mit.edu/lauren/publications/odonnell_WMTractAtlas_ismrm2006.pdf

Parker Jamie B. , Daniel S. Marcus, Tracy H. Wang, Abraham Z. Snyder, Laura E. Girton, John C. Morris, Randy L. Buckner, Open Access Structural Imaging Series (OASIS), Alzheimer's and Dementia, 2:S681-S682, 2006.

Turner J. A , C. Fennema-Notestine, M. E. Martone, A. R. Laird, J. S. Grethe, W. Bug, A. Gupta, C. Bean. You say potato, I say potahto: Ontological engineering applied within the Biomedial Informatics Research Network, Society for Neuroscience Annual Meeting (2006).

2005

Bakshi, K and Karger DR, End-User Application Development for the Semantic Web. International Semantic Web Conference, November 6, 2005, Galway, Ireland.

Bakshi, K and Karger DR, Semantic Web Applications. International Semantic Web Conference, November 6, 2005, Galway, Ireland.

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, BIRN Brain Morphometry (2005) "Pattern classification of hippocampal shape analysis in a study of Alzheimer's Disease." In: Human Brain Mapping Conference.

Fennema-Notestine, C., Gollub, R., Fischl, B., Quinn, B. T., Pacheco, J., Gamst, A. C., Feasibility of multi-site clinical structural neuroimaging studies of legacy data: Aging and Alzheimer's disease. et al. Society for Neuroscience. Washington, D.C. Program No. 410.5 (2005).

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, the Morphometry BIRN, Brown GG (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. (PDF)

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

Jovicich J, Czanner S, Han X, Greve D, Pacheco J, Busa1 E, van der Kouwe A, Fischl B, Dale A, Reproducibility of automated brain morphometric estimates derived from multi-site structural MRI studies. International Society of Magnetic Resonance in Medicine, 13th Annual Meeting, Miami, Florida May 7-13, 2005.

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.

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.

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, Miller MI (2004) "Biomedical Informatics Research Network: Multi-site Processing pipeline for shape analysis of brain structures." In: Human Brain Mapping. Budapest. (Poster PDF)

Bischoff-Grethe A, Fischl B, Ozyurt IB, Morris S, Brown GG, Fennema-Notestine C, Clark CP, Bondi MW, Jernigan TL, Brain Morphometry BIRN (2004) "A technique for the deidentification of structural brain MR images." Human Brain Mapping. Budapest. Jun 2004. (Poster 2 PDF, Abstract PDF)

Fischl B, Salat DH, van der Kouwe AJW, Makris N, Ségonne F, Dale AM (2004) "Sequence-Independent Segmentation of Magnetic Resonance Images, Neuroimage." Jul 2004 (Abstract PDF)

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

Marcus DM, Olsen TR, Ramaratnam M, Buckner R (2004) "XNAT: A software framework for managing neuroimaging laboratory data." In: Society for Neuroscience. San Diego. (Abstract)

Marcus DM, Olsen T, Ramaratnam M, Snyder A, Buckner R (2004) "XNAT - The extensible neuroimaging archive toolkit: informatics tools for managing and exploring neuroimaging data." In: Human Brain Project Annual Conference, NIH. Bethesda, MD.

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." Human Brain Mapping, Budapest. (Abstract PDF)

Ozyurt IB, Brown GG, Grethe JS, Morphometry BIRN, FIRST BIRN (2004) "A general, extensible system for human brain imaging data retrieval and maintenance." Human Brain Mapping. Budapest. Jun 2004. (Abstract PDF)

2003

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

2002

2007

Bischoff-Grethe A, Ozyurt IB, Busa E, Quinn BT, Fennema-Notestine C, Clark CP, Morris S, Bondi MW, Jernigan TL, Brown GG, and Fischl B. A technique for the deidentification of structural brain MR images. Human Brain Mapping (in press) 2006.

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

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).

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.

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)

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

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.

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

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, Brown GG. (2006) Quantitative evaluation of automated skull-stripping methods applied to contemporary and legacy images: Effects of diagnosis, bias correction, and slice location. Human Brain Mapping 2006 Feb;27(2):99-113.

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, Fischl B. Reliability of MRI-derived measurements of human cerebral cortical thickness: the effects of field strength, scanner upgrade and manufacturer. Neuroimage. 2006 Aug 1;32(1):180-94.

Jovicich J, Czanner S, Greve D, Haley E, van der Kouwe A, Gollub R, Kennedy D, Schmitt F, Brown G, Macfall J, Fischl B, Dale A. Reliability in multi-site structural MRI studies: effects of gradient non-linearity correction on phantom and human data. Neuroimage. 2006 Apr 1;30(2):436-43.

MacFall, J. R., Taylor, W. D., Rex, D. E., Pieper, S., Payne, M. E., McQuoid, D. R., Steffens, D. C., Kikinis, R., Toga, A. W., and Krishnan, K. R. Lobar distribution of lesion volumes in late-life depression: the Biomedical Informatics Research Network (BIRN). Neuropsychopharmacology, 31: 1500-1507, 2006.

Marcus, D.S., Olsen T., Ramaratnam M., and Buckner, R.L., The Extensible Neuroimaging Archive Toolkit (XNAT): An informatics platform for managing, exploring, and sharing neuroimaging data. Neuroinformatics, in press, 2006.

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

van der Kouwe A, Benner T, Dale A. Real-Time Prospective Rigid Body Motion Correction and Shimming Using Clover-Leaf Navigators. Magnetic Resonance in Medicine (in press) 2006.

2005

Chen B, Guo H, Song AW. Correction for direction-dependent distortions in diffusion tensor imaging using matched magnetic field maps. Neuroimage. 2006 Mar;30(1):121-9. Epub 2005 Oct 20.

Jovicich J, Beg MF, Pieper S, Priebe C, Miller MM, Buckner R, Rosen B, Morphometry BIRN (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.

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.

2004

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, Dale AM (2004) Automatically parcellating the human cerebral cortex. Cereb Cortex 14:11-22.

2003

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

Peltier ST, Ellisman MH (2003) "The Biomedical Informatics Research Network". The Grid, Blueprint for a New Computing Infrastructure. 2nd edition: Elsevier (in press).

Santini S, Gupta A (2003) "The role of Internet Imaging in the Biomedical Informatics Research Network." Proceedings of SPIE, Vol. 5018 (Santini S, Schettini R eds.) San Jose: Internet Imaging IV, January (PDF)

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, Dale AM. (2002) Whole brain segmentation: automated labeling of neuroanatomical structures in the human brain. Neuron 33:341-355.

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

2001

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

2000

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

1999

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

Fischl B, Sereno MI, Dale AM (1999) "Cortical surface-based analysis II: inflation, flattening, and a surface-based coordinate system." NeuroImage. 1999.

Fischl B, Sereno MI, Tootell RBH, Dale AM (1999) "High-resolution inter-subject averaging and a coordinate system for the cortical surface". Hum Brain Map. 1999.

2006

Farrell J.A.D, Landman B.A., Jones C.K., Smith S.A.,Prince J.L., van Zijl P.C.M, Mori S. "Effects of Diffusion Weighting Scheme and SNR on DTI-derived Fractional Anisotropy at 1.5T" (poster) in Proceedings of the 14th Annual Scientific Meeting of the International Society for Magnetic Resonance in Medicine, Seattle WA, May 2006.

Farrell J.A.D., Landman B.A., Jones C.K., Smith S.A., Prince J.L., van Zijl P.C.M., Mori S. "Effects of Scan Repetition on DTI-derived Fractional Anisotropy Measures at 1.5T" (poster) ISMRM workshop: Imaging Myelin: Formation, Destruction and Repair, Vancouver BC, February 2006.

Landman B.A., Farrell J.A.D., Mori S, Prince J.L. "A Novel Method of Partitioning Diffusion Weighted Schemes for Efficient Comparison of DTI Protocols" (poster) in Proceedings of the 14th Annual Scientific Meeting of the International Society for Magnetic Resonance in Medicine, Seattle WA, May 2006.

Landman B.A., Farrell J.A.D., Mori S, van Zijl P.C.M., Prince J.L. "On the Coregistration of Diffusion Weighted Images" (poster) in Proceedings of the 14th Annual Scientific Meeting of the International Society for Magnetic Resonance in Medicine, Seattle WA, May 2006.

2005

Beg et al., (2005). "Pattern classification of hippocampal shape analysis in a study of Alzheimer's Disease." Human Brain Mapping Conference. (PDF)

Fennema-Notestine C, Gollub R, Fischl B, Quinn BT, Pacheco J, Dickerson B, (2005) "Feasibility of multi-site clinical structural neuroimaging studies of legacy data: Aging & Alzheimer's disease." Society for Neuroscience 2005. (PDF)

Han et al., (2005) "CNR Comparison of three pulse sequences for structural MR Brain Imaging." 2005 Human Brain Mapping Conference. (PDF)

Jovicich et al. (2005) "Biomedical Informatics Research Network: Integrating Multi-Site Neuroimaging Data Acquisition, Data Sharing and Brain Morphometric Processing." The 18th IEEE International Symposium on Computer-Based Medical Systems (IEEE CBMS 2005) (PDF)

Jovicich et al., (2005) "Test-retest reliability assessment for longitudinal MRI studies: An intensity-based comparison of T1-weighted protocols and field strengths." 2005 Human Brain Mapping Conference. (PDF)

Jovicich et al.,(2005) "Test-retest reproducibility assessments for longitudinal studies: quantifying MRI system upgrade effects." International Society of Magnetic Resonance in Medicine, Miami May 2005. (PDF)

Quinn et al., (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." 2005 Human Brain Mapping Conference. (PDF)

2004

Marcus DM, Olsen T, Ramaratnam M, Snyder A, Buckner R (2004) "XNAT - The extensible neuroimaging archive toolkit: informatics tools for managing and exploring neuroimaging data." In: Human Brain Project Annual Conference, NIH. Bethesda, MD.

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. (Poster PDF)

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

2003

Jovicich J, Pieper S, Miller MI, Gollub RL, Rex D, Bischoff-Grethe A, Buckner R, Krishnan R (2003) "Brain Morphometry BIRN - Integrating Multi-Site Human Neuroimaging Data, Data Acquisition, Data Sharing and Brain Morphometry Processing". In: BISTIC. (Poster)

Kirby FM (2003) "BIRN - Computational Anatomy on the Geometries of the Brain, Medical Image Data, Data Analysis Pipeline, Large Deformation Metric Mapping, and Storage Resource Broker" 2003. In: Research Center for Functional Brain Imaging. Center for Imaging Science (CIS). (Poster)

Fennema-Notestine C, Ozyurt IB, Brown GG, Clark CP, Morris S, Bischoff-Grethe A, Bondi MW, Jernigan TL, Brain Morphometry BIRN (2003) "Bias Correction, Pulse Sequence, And Neurodegeneration Influence Performance Of Automated Skull-Stripping Methods." Society for Neuroscience, New Orleans, 2003.

Shattuck D, Rex DE, Darvas F, Leahy R, Toga AW (2003) "JohnDoe: Anonymizing MRI Data for the Protection of Research Subject Confidentiality." Human Brain Mapping. New York, 2003. Poster number: 942.