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Methods

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Published material describing the methods used in FreeSurfer (please cite our software!, see also boilerplate text):

surface reconstruction

• Cortical Surface-Based Analysis I: Segmentation and Surface Reconstruction, Dale, A.M., Fischl, B., Sereno, M.I., (1999). NeuroImage 9(2):179-194

• Cortical Surface-Based Analysis II: Inflation, Flattening, and a Surface-Based Coordinate System, Fischl, B., Sereno, M.I., Dale, A.M., (1999). NeuroImage, 9(2):195-207.

• Automated Manifold Surgery: Constructing Geometrically Accurate and Topologically Correct Models of the Human Cerebral Cortex, Fischl, B., Liu, A. and Dale, A.M., (2001). IEEE Transactions on Medical Imaging, 20(1):70-80.

• Improved localization of cortical activity by combining EEG and MEG with MRI cortical surface reconstruction: A linear approach, Dale, A.M., and Sereno, M.I. (1993). Journal of Cognitive Neuroscience 5:162-176.

• A Hybrid Approach to the Skull-Stripping Problem in MRI, Ségonne, F., Dale, A.M., Busa, E., Glessner, M., Salvolini, U., Hahn, H.K., Fischl, B. (2004). NeuroImage, 22:1160-1075.

• Genetic Algorithm for the Topology Correction of Cortical Surfaces, F. Segonne, E. Grimson, B. Fischl (2005). IPMI pp393--405.

inter-subject spherical averaging

• High-resolution inter-subject averaging and a coordinate system for the cortical surface, Fischl, B., Sereno, M.I., Tootell, R.B.H., and Dale, A.M., (1999). Human Brain Mapping, 8:272-284(1999).

• Learning Task-Optimal Registration Cost Functions for Localizing Cytoarchitecture and Function in the Cerebral Cortex, B.T. Yeo, M.R. Sabuncu, T. Vercauteren, D. Holt, K. Amunts, K. Zilles, P. Golland, B. Fischl. IEEE Transactions on Medical Imaging, 29(7):1424--1441, 2010

• Spherical Demons: Fast Diffeomorphic Landmark-Free Surface Registration, B.T. Yeo, Mert R. Sabuncu, Tom Vercauteren, Nicholas Ayache, Bruce Fischl, Polina Golland (2010). IEEE TRANSACTIONS ON MEDICAL IMAGING. 29(3):650–668, 2010

thickness measurement

• Measuring the Thickness of the Human Cerebral Cortex from Magnetic Resonance Images, Fischl, B., and Dale, A.M., (2000). Proceedings of the National Academy of Sciences, 97:11044-11049.

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

• see also below: Rosas et al. (histology) and Kuperberg et al. (MRI) were validation studies for the thickness measures

cortical parcellation

• Automatically Parcellating the Human Cerebral Cortex, Fischl, B., A. van der Kouwe, C. Destrieux, E. Halgren, F. Segonne, D. Salat, E. Busa, L. Seidman, J. Goldstein, D. Kennedy, V. Caviness, N. Makris, B. Rosen, and A.M. Dale, (2004). Cerebral Cortex, 14:11-22.

• An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest, Desikan, R.S., F. Segonne, B. Fischl, B.T. Quinn, B.C. Dickerson, D. Blacker, R.L. Buckner, A.M. Dale, R.P. Maguire, B.T. Hyman, M.S. Albert, and R.J. Killiany, (2006). NeuroImage 31(3):968-80.

• Cortical Folding Patterns and Predicting Cytoarchitecture, Fischl, B., N. Rajendran, E. Busa, J. Augustinack, O. Hinds, B.T. Yeo, H. Mohlberg, K. Amunts, and K. Zilles, Cerebral Cortex, 2008. 18(8): p. 1973-80.

• Effects of Registration Regularization and Atlas Sharpness on Segmentation Accuracy, B.T. Yeo, M.R. Sabuncu, R. Desikan, B. Fischl and P. Golland. Medical Image Analysis, 12(5):603:615, 2008.

• A sulcal depth-based anatomical parcellation of the cerebral cortex, C. Destrieux, B. Fischl, A. Dale, E. Halgren (2009). Human Brain Mapping 2009.

• Automatic parcellation of human cortical gyri and sulci using standard anatomical nomenclature, C. Destrieux, B. Fischl, A. Dale, E. Halgren (2010). NeuroImage 53(1): 1-15.

subcortical segmentation

• Whole Brain Segmentation: Automated Labeling of Neuroanatomical Structures in the Human Brain, Fischl, B., D.H. Salat, E. Busa, M. Albert, M. Dieterich, C. Haselgrove, A. van der Kouwe, R. Killiany, D. Kennedy, S. Klaveness, A. Montillo, N. Makris, B. Rosen, and A.M. Dale, (2002). Neuron, 33:341-355.

• Sequence-Independent Segmentation of Magnetic Resonance Images, Fischl, B., Salat, D.H., van der Kouwe, A.J.W., Makris, N., Ségonne, F., and Dale, A.M. (2004) NeuroImage 23:S69-S84.

• Atlas Renormalization for Improved Brain MR Image Segmentation Across Scanner Platforms, Han, X. and B. Fischl, (2007). IEEE Transactions on Medical Imaging, 26(4):479-486.

longitudinal processing

• Highly Accurate Inverse Consistent Registration: A Robust Approach, M. Reuter, H.D. Rosas, B. Fischl, (2010). NeuroImage 53 (4):1181-1196.

• Avoiding asymmetry-induced bias in longitudinal image processing, M. Reuter, B. Fischl, (2011). NeuroImage 57 (1):19-21.

• Please cite this if you run the longitudinal stream in Freesurfer version 4.3 or later: Within-Subject Template Estimation for Unbiased Longitudinal Image Analysis, M. Reuter, N.J. Schmansky, H.D. Rosas, B. Fischl, (2012), NeuroImage 61(4):1402-1418.

• Statistical Analysis of Longitudinal Neuroimage Data with Linear Mixed Effects Models, J.L. Bernal-Rusiel, D.N. Greve, M. Reuter, B. Fischl, M.R. Sabuncu, NeuroImage (2012), doi: 10.1016/j.neuroimage.2012.10.065

• Spatiotemporal Linear Mixed Effects Modeling for the Mass-univariate Analysis of Longitudinal Neuroimage Data, J.L. Bernal-Rusiel, M. Reuter, D.N. Greve, B. Fischl, M.R. Sabuncu, NeuroImage (2013), doi: 10.1016/j.neuroimage.2013.05.049

related methodological papers

• Discriminative Analysis for Image-Based Studies, Golland, P., B. Fischl, M. Spiridon, N. Kanwisher, R.L. Buckner, M.E. Shenton, R. Kikinis, A. Dale, W.E.L. Grimson, (2002) In Proc. MICCAI'2002: Fifth International Conference on Medical Image Computing And Computer Assisted Intervention. LNCS 2488:508-515.

• Permutation Tests for Classification: Towards Statistical Significance in Image-Based Studies, Golland P., and B. Fischl, (2003) Proc. IPMI2003: 18th International Conference on Information Processing in Medical Imaging.

• Topology Correction of Subcortical Segmentation, Segonne, F., E. Grimson and B. Fischl, (2003) MICCAI 2003.

• A unified approach for morphometric and functional data analysis in young, old, and demented adults using automated atlas-based head size normalization: reliability and validation against manual measurement of total intracranial volume, Buckner, R.L., D. Head, J. Parker, A.F. Fotenos, D. Marcus, J.C. Morris, and A.Z. Snyder (2004) NeuroImage 23:724-738.

• Reliability in Multi-Site Structural MRI Studies: Effects of Gradient Non-linearity Correction on Phantom and Human Data, Jovicich J, Czanner S, Greve D, Haley E, Kouwe A, Gollub R, Kennedy D, Schmitt F, Brown G, MacFall J, Fischl B, Dale A., (2006) NeuroImage, 30(2): 436-443.

• Geometrically Accurate Topology-Correction of Cortical Surfaces Using Nonseparating Loops, Segonne, F., J. Pacheco, B. Fischl, (2007) IEEE Transactions on Medical Imaging, 26(4):518-529.

• Phase maps reveal cortical architecture, Bruce Fischl and Lawrence L. Wald, PNAS, July 10, 2007, vol. 104, no. 28.

• What Data to Co-register for Computing Atlases, B.T.T. Yeo, M. Sabuncu, H. Mohlberg, K. Amunts, K. Zilles, P. Golland, B. Fischl (2007). Proceedings of the IEEE Computer Society Workshop on Mathematical Methods in Biomedical Image Analysis (MMBIA 2007).

• A Technique for the Deidentification of Structural Brain MR Images, Bischoff-Grethe, A., I.B. Ozyurt, E. Busa, B.T. Quinn, C. Fennema-Notestine, C.P. Clark, S. Morris, M.W. Bondi, T.L. Jernigan, A.M. Dale, G.G. Brown, and B. Fischl (2007) Human Brain Mapping, volume 28, issue 9, pp 892-903.

• An MRI-based method for measuring volume, thickness and surface area of entorhinal, perirhinal, and posterior parahippocampal cortex, Feczko, E., J.C. Augustinack, B. Fischl, B.C. Dickerson, (2007). Neurobiology of Aging, 2007 Sep 10.

• Brain morphometry with multiecho MPRAGE, van der Kouwe, A.J.W., T. Benner, D.H. Salat, and B. Fischl (2008). NeuroImage 40 (2008) 559-569.

• Accurate prediction of V1 location from cortical folds in a surface coordinate system, Hinds, O.P., N. Rajendran, J.R. Polimeni, J.C. Augustinack, G. Wiggins, L.L. Wald, H.D. Rosas, A. Potthast, E.L. Schwartz and B. Fischl (2008). NeuroImage 39:1585-1599.

• A Surface-Based Approach to Quantify Local Cortical Gyrification, Schaer, M., M. Bach Cuadra, L. Tamarit, F. Lazeyras, S. Eliez, and J.P. Thiran (2008). IEEE Transactions on Medical Imaging, Vol. 27, No. 2, February 2008. See also: JoVE video

• On the Construction of Invertible Filter Banks on the 2-Sphere. B.T. Yeo, W. Ou, P. Golland. IEEE Transactions on Image Processing, 17(3):283--300, 2008.

• Reliability of MRI-derived cortical and subcortical morphometric measures: Effects of pulse sequence, voxel geometry, and parallel imaging, Wonderlick, J.S., D.A. Ziegler, P. Hosseini-Varnamkhasti, J.J. Locascio, A. Bakkour, A. van der Kouwe, C. Triantafyllou, S. Corkin, and B.C. Dickerson. NeuroImage 44 (2009) 1324–1333.

• MRI-derived measurements of human subcortical, ventricular and intracranial brain volumes: Reliability effects of scan sessions, acquisition sequences, data analyses, scanner upgrade, scanner vendors and field strengths, Jovicich, J., S. Czanner, X. Han, D. Salat, A. van der Kouwe, B. Quinn, J. Pacheco, M. Albert, R. Killiany, D. Blacker, P. Maguire, D. Rosas, N. Makris, R. Gollub, A. Dale, B.C. Dickerson, and B. Fischl (2009). NeuroImage 46 (2009) 177–192.

• Automated Segmentation of Hippocampal Subfields From Ultra-High Resolution In Vivo MRI, K. V. Leemput, A. Bakkour, T. Benner, G. Wiggins, L. L. Wald, J. Augustinack, B. C. Dickerson, P. Golland, B. Fischl (2009). Hippocampus 19:549–557 (2009)

• Accurate and robust brain image alignment using boundary-based registration, D. Greve and B. Fischl, NeuroImage, Volume 48, Issue 1, 15 October 2009, Pages 63-72.

• Combined Volumetric and Surface Registration, G.Postelnicu, L.Zollei, B. Fischl(2009). IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 28, NO. 4, APRIL 2009

• Skull Stripping Using Graph Cuts, S.A. Sadananthan, W. Zheng, M.W.L. Chee, and V. Zagorodnov (2010). NeuroImage, 49:1, 225–239, 2010.

• A Generative Model for Image Segmentation Based on Label Fusion, Mert R. Sabuncu, B.T. Thomas Yeo, Koen Van Leemput, Bruce Fischl, Polina Golland (2010). IEEE Transactions on Medical Imaging, 2010.

• Learning Task-Optimal Registration Cost Functions for Localizing Cytoarchitecture and Function in the Cerebral Cortex, B.T. Thomas Yeo, Mert R. Sabuncu, Tom Vercauteren, Daphne J. Holt, Katrin Amunts, Karl Zilles, Polina Golland and Bruce Fischl (2010). IEEE TRANSACTIONS ON MEDICAL IMAGING, TO BE PUBLISHED.

• Automated probabilistic reconstruction of white-matter pathways in health and disease using an atlas of the underlying anatomy, Yendiki A, Panneck P, Srinivasan P, Stevens A, Zöllei L, Augustinack J, Wang R, Salat D, Ehrlich S, Behrens T, Jbabdi S, Gollub R and Fischl B (2011). Front. Neuroinform. 5:23. doi: 10.3389/fninf.2011.00023.

• Entorhinal verrucae correlate with surface geometry, Augustinack JC, Huber KE, Postelnicu GM, Frosch MP, Pienaar R, Fischl B.,(2012). Translational Neuroscience, 3(2), 123-131 doi: 10.2478/s13380-012-0019-8.

• The Relevance Voxel Machine (RVoxM): A Self-tuning Bayesian Model for Informative Image-based Prediction, Sabuncu M, Van Leemput K (2012). IEEE Trans Med Imaging, [Epub ahead of print].

• On Removing Interpolation and Resampling Artifacts in Rigid Image Registration, Aganj I, Yeo BTT, Sabuncu MR, Fischl B, (2013). IEEE Transactions on Image Processing, 22(2):816--827, doi: 10.1109/TIP.2012.2224356.

history

• FreeSurfer, Fischl B (2012). NeuroImage 62(2):774-781.

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Citations

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Published material citing Freesurfer:

(If you have a citation you would like to include in this list please e-mail your request to vinke[at]nmr.mgh.harvard.edu)

cortical thickness

• Regional and progressive thinning of the cortical ribbon in Huntington's disease, Rosas, H.D., A.K. Liu, S. Hersch, M. Glessner, R.J. Ferrante, D.H. Salat, A. van der Kouwe, B.G. Jenkins, A.M. Dale, and B. Fischl, (2002). Neurology, 58:695-701.

• Regionally localized thinning of the cerebral cortex in schizophrenia, Kuperberg, G.R., M.R. Broome, P.K. McGure, A.S. David, M. Eddy, F. Ozawa, D. Goff, C. West, S.C.R. WIlliams, A.J.W. van der Kouwe, D.H. Salat, A.M. Dale, and B. Fischl, (2003). Archives of General Psychiatry, 60:878-888.

• Focal thinning of the cerebral cortex in multiple sclerosis, Sailer, M., B. Fischl, D. Salat, C. Tempelmann, M. Schonfeld, E. Busa, N. Bodammer, H. Heinze, and A. Dale, (2003). Brain, 126(9):1734-1744. (See also: editorial)

• Thinning of the Cerebral Cortex in Aging, D.H. Salat, R.L. Buckner, A.Z. Synder, R.S.R. Desikan, D.N. Greve, E. Busa, J.C. Morris, A.M. Dale, and B. Fischl, (2004). Cerebral Cortex, 14:721-730.

• A magnetic resonance imaging study of cortical thickness in animal phobia, Rauch, S., C. Wright, B. Martis, E. Busa, K. McMullin, L. Shin, A. Dale, and B. Fischl, (2004). Biological Psychiatry, 55(9):946-952.

• Differing neuropsychological and neuroanatomical correlates of abnormal reading in early-stage semantic dementia and dementia of the Alzheimer type, Gold, B.T., D.A. Balota, M.J. Cortes, S.D. Sergent-Marshall, A.Z. Snyder, D.H. Salat, B. Fischl, A.M. Dale, J.C. Morris, and R.L. Buckner, (2005). Neuropsychologia, 43: p. 833-846.

• Thickness of ventromedial prefrontal cortex in humans is correlated with extinction memory, Milad, M.R., B.T. Quinn, R.K. Pitman, S.P. Orr, B. Fischl, and S.L. Rauch (2005). PNAS, 102(30):10706-10711.

• Meditation experience is associated with increased cortical thickness, Lazar, S.W., C.E. Kerr, R.H. Wasserman, J.R. Gray, D.N. Greve, M.T. Treadway, M. McGarvey, B.T. Quinn, J.A. Dusek, H. Benson, S.L. Rauch, C.I. Moore, and B. Fischl, (2005). NeuroReport, 16(17): 1893-1897.

• Selective increase of cortical thickness in high-performing elderly - structural indices of optimal cognitive aging, Fjell, A.M., K.B. Walhovd, I. Reinvang, A. Lundervold, D. Salat, B.T. Quinn, B. Fischl and A.M. Dale (2006). NeuroImage 29:984-994.

• Regional cortical thickness matters in recall after months more than minutes, Walhovd, K.B., A.M. Fjell, A.M. Dale, B. Fischl, B.T. Quinn, N. Makris, D. Salat, and I. Reinvan (2006). NeuroImage 31:1343 - 1351.

• Mapping an intrinsic MR property of gray matter in auditory cortex of living humans: A possible marker for primary cortex and hemispheric differences, Sigalovsky, I.S., B. Fischl, and J.R. Melchera (2006). NeuroImage 32:1524-1537.

• Anatomical differences in the mirror neuron system and social cognition network in autism, Hadjikhani N., R.M. Joseph, J. Snyder, H. Tager-Flusberg (2006). Cerebral Cortex 16(9):1276-82.

• Neuroanatomical Correlates of Extraversion and Neuroticism, Wright, C.I., D. Williams, E. Feczko, L. Feldman Barrett, B.C. Dickerson, C.E. Schwartz, and M.M. Wedig (2006). Cerebral Cortex 2006;16:1809--1819.

• Neuroimaging H.M.: A 10-Year Follow-Up Examination, Salat, D.H., A.J.W. van der Kouwe, D.S. Tuch, B.T. Quinn, B. Fischl, A.M. Dale and S. Corkin (2006). HIPPOCAMPUS 16:936–945 (2006).

• Different regional patterns of cortical thinning in Alzheimer's disease and frontotemporal dementia, Du, AT, N. Schuff, J.H. Kramer, H.J. Rosen, M.L. Gorno-Tempini, K. Rankin, B.L. Miller and M.W. Weiner (2007). Brain 130:1159-1166.

• Differential effects of aging and Alzheimer's disease on medial temporal lobe cortical thickness and surface area, Dickerson B.C, E. Feczko, J.C. Augustinack, J. Pacheco, J.C. Morris, B. Fischl, R.L. Buckner (2007). Neurobiology of Aging, 2007 Sep 13.

• Thickening in the somatosensory cortex of patients with migraine, DaSilva, A.F.M., C. Granziera, J. Snyder and N. Hadjikhani (2007). Neurology 69:1990-1995.

• Abnormal cerebral cortex structure in children with ADHD, Wolosin S.M., Richardson M.E., Hennessey J.G., Denckla M.B., Mostofsky S.H. Human Brain Mapping, 2007 Nov 5.

• Cognitive Function, P3a/P3b Brain Potentials, and Cortical Thickness in Aging, Fjell, A.M. K.B. Walhovd, B. Fischl and I. Reinvang. Human Brain Mapping 28:1098–1116 (2007).

• Changes in cerebral cortex of children treated for medulloblastoma, Liu AK, Marcus KJ, Fischl B, Grant PE, Poussaint TY, Rivkin MJ, Davis P, Tarbell NJ, Yock TI (2007). Int J Radiat Oncol Biol Phys. 2007 Jul 15;68(4):992-8. Epub 2007 Mar 26. PMID: 17379433 [PubMed - indexed for MEDLINE]

• Detection of cortical thickness correlates of cognitive performance: Reliability across MRI scan sessions, scanners, and field strengths, Dickerson, B.C., E. Fenstermacher, D.H. Salat, D.A. Wolk, R.P. Maguire, R. Desikan, J. Pacheco, B.T. Quinn, A. Van der Kouwe, D.N. Greve, D. Blacker, M.S. Albert, R.J. Killiany, and B. Fischl (2008). NeuroImage 39(1):10-8.

• Cerebral cortex and the clinical expression of Huntington's disease: complexity and heterogeneity, Rosas, D.H., D.H. Salat, S.Y. Lee, A.K. Zaleta, V. Pappu, B. Fischl, D. Greve, N. Hevelone and S.M. Hersch (2008). Brain doi:10.1093/brain/awn025.

• Regional neocortical thinning in mesial temporal lobe epilepsy, McDonald, C.R., D.J. Hagler, Jr., M.E. Ahmadi, E. Tecoma, V. Iragui, L. Gharapetian, A.M. Dale, and E. Halgren (2008). Epilepsia 48 (2), 211-219.

• Morphometric Changes in the Episodic Memory Network and Tau Pathologic Features Correlate With Memory Performance in Patients With Mild Cognitive Impairment, A.M.Fjell, K.B.Walhovd, I.Amlien, A. Bjørnerud, I.Reinvang, L.Gjerstad, T.Cappelen, F.Willoch, P. Due-Tønnessen, R.Grambaite, A.Skinningsrud, V.Stenset, T.Fladby. AJNR Am J Neuroradiol, Jun-Jul 2008.

• Accelerated age-related cortical thinning in healthy carriers of apolipoprotein E ε4, Espeseth T., L.T. Westlye, A.M. Fjell, K.B. Walhovd, H. Rootwelt, I. Reinvanga. Neurobiology of Aging 29 (2008) 329–340.

• Regional thinning of the cerebral cortex in schizophrenia: Effects of diagnosis, age and antipsychotic medication, Nesvåg, R., G. Lawyer, K. Varnäs, A.M. Fjell, K.B. Walhovd, A. Frigessi, E.G. Jönsson, I. Agartz. Schizophrenia Research 98 (2008) 16 – 28.

• Evidence for abnormalities of cortical development in Adolescent-Onset Schizophrenia, Voets, N.L., M. Hough, G. Douaud, P.M. Matthews, A. James, L. Winmill, P. Webster, S. Smith (2008). NeuroImage, doi: 10.1016/j.neuroimage.2008.08.013.

• Colocalized Structural and Functional Changes in the Cortex of Patients with Trigeminal Neuropathic Pain, DaSilva, A.F., L. Becerra, G. Pendse, B. Chizh, S. Tully, D. Borsook (2008). PLoS ONE. 2008; 3(10): e3396. (sup 1, sup 2)

• Cortical thickness reduction of normal appearing cortex in patients with polymicrogyria, Oliveira Jr, Pedro Paulo; Leite, Claudia; Valente, Kette; Shergill, Sukhwinder; Amaro Jr, Edson (2008). Journal of Neuroimaging - 2008 - In Press

• Diffuse changes in cortical thickness in pediatric moderate-to-severe traumatic brain injury, Merkley, T.L., Bigler, E.D., Wilde, E.A., McCauley, S.R., Hunter, J.V. and Levin, H.S. (2008). J Neurotrauma 25(11):1343-1345.

• The complex minds of teenagers: Neuroanatomy of personality differs between sexes Blankstein, U., J.Y.W. Chena,, A.M. Mincicd, P.A. McGrathc, K.D. Davis (2008). Neuropsychologia 47 (2009) 599–603.

• Detection of focal changes in human cortical thickness: Spherical wavelets thresholding versus Gaussian smoothing. Bernal-Rusiel JL, Atienza M, Cantero JL (2008). Neuroimage, 41:1278-1292.

• The Cortical Signature of Alzheimer's Disease: Regionally Specific Cortical Thinning Relates to Symptom Severity in Very Mild to Mild AD Dementia and is Detectable in Asymptomatic Amyloid-Positive Individuals, Bradford C. Dickerson, Akram Bakkour, David H. Salat, Eric Feczko, Jenni Pacheco, Douglas N. Greve, Fran Grodstein, Christopher I. Wright, Deborah Blacker, H. Diana Rosas, Reisa A. Sperling, Alireza Atri, John H. Growdon, Bradley T. Hyman, John C. Morris, Bruce Fischl, and Randy L. Buckner (2009). Cerebral Cortex 2009 19: 497-510; doi:10.1093/cercor/bhn113

• Distinct Genetic Influences on Cortical Surface Area and Cortical Thickness, Matthew S. Panizzon; Christine Fennema-Notestine; Lisa T. Eyler; Terry L. Jernigan; Elizabeth Prom-Wormley; Michael Neale; Kristen Jacobson; Michael J. Lyons; Michael D. Grant; Carol E. Franz; Hong Xian; Ming Tsuang; Bruce Fischl; Larry Seidman; Anders Dale; William S. Kremen (2009). Cerebral Cortex 2009; doi: 10.1093/cercor/bhp026

• Anatomical atlas-guided diffuse optical tomography of brain activation, Anna Custo, David A. Boas, Daisuke Tsuzuki, Ippeita Dan, Rickson Mesquita, Bruce Fischl, W. Eric L. Grimson, Williams Wells III (2009). NeuroImage 2009. YNIMG-06435

• Cortical thickness and voxel-based morphometry in posterior cortical atrophy and typical Alzheimer's disease (2009). Lehmann M, Crutch SJ, Ridgway GR, Ridha BH, Barnes J, Warrington EK, Rossor MN, Fox NC (2009). Neurobiology of Aging, 2009 Sep 24.

• Age-associated alterations in cortical gray and white matter signal intensity and gray to white matter contrast, D.H.Salat, S.Y.Lee, A.J.van der Kouwe, D.N.Greve, B.Fischl, H.D.Rosas (2009). NeuroImage, 2009. YNIMG-06406; No. of pages: 8; 4C: 3, 4, 5, 6

• Cortical thickness or grey matter volume? The importance of selecting the phenotype for imaging genetics studies, A.M. Winkler, P.Kochunov, J.Blangero, L.Almasy, K.Zilles,. P.T. Fox, R.Duggirala and D.C. Glahn (2009). doi:10.1016/j.neuroimage.2009.12.028

• Regionally Specific Cortical Thinning in Children with Sickle Cell Disease, G.R.Kirk, M.R.Haynes, S.Palasis, C.Brown, T.G.Burns, M.McCormick, R.A.Jones (2008). Cerebral Cortex July 2009;19:1549--1556

• Prefrontal plasticity and stress inoculation-induced resilience, Katz, M., C. Liu, M. Schaer, K. J. Parker, M.-C. Ottet, A. Epps, C. L. Buckmaster, R. Bammer, M. E. Moseley, A. F. Schatzberg, S. Eliez, D. M. Lyons (2009). Dev Neurosci. 31(4):293-9.

• Cognitive function and brain structure correlations in healthy elderly East Asians, MWL Chee, KHM Chen, H Zheng, KPL Chan, Lisa Y.M. Chuah, M. Schuchinsky, B. Fischl and Tze Pin Ng (2009). Neuroimage, 2009.

• Progressive logopenic/phonological aphasia: erosion of the language network. Rohrer, J.D., Ridgway, G.R., Crutch, S.J., Hailstone, J., Goll, J.C., Clarkson, M.J., Mead, S., Beck, J., Mummery, C., Ourselin, S., Warrington, E.K., Rosser, M.N. and Warren, J.D. (2009) Neuroimage 49 (1):984-93

• Patterns of cortical thickness according to APOE genotype in Alzheimer's disease. Gutierrez-Galve, L., Lehmann, M., Hobbs, N.Z., Clarkson, M.J., Ridgway, G.R., Crutch, S., Ourselin, S., Schott, J.M., Fox, N.C. and Barnes, J. (2009) Dement Geriatr Cogn Disord 28(5):476-85

• Cortical Thickness Reduction of Normal Appearing Cortex in Patients with Polymicrogyria, Oliveira Jr., P.P.M., K.D. Valente, S.S. Shergill, C.C. Leite, E. Amaro Jr. (2010). J Neuroimaging 2010;20:46-52.

• Structural Differences in Adult Orbital and Ventromedial Prefrontal Cortex Predicted by Infant Temperament at 4 Months of Age, Carl E. Schwartz. MD, Pratap S. Kunwar. MS, Douglas N. Greve. PhD, Lyndsey R. Moran, BA, Jane C. Viner. BA, Jennifer M. Covino. BS, MPA, Jerome Kagan. PhD, S. Evelyn Stewart. MD, Nancy C. Snidman. PhD, Mark G. Vangel. PhD, Stuart R. Wallace. BS. (2010). Arch Gen Psychiatry. 2010;67(1):78-84

• MET Variant Of The Catechol-O-MethylTransferase Genotype Is Associated With Thicker Cortex In Adult Brain, A. Cerasa, A. Cherubini, A. Quattrone, M.C. Gioia, P. Tarantino, G. Annesi, F. Assogna, C. Caltagirone and G. Spalletta (2010). Neuroscience(2010), doi: 10.1016/j.neuroscience.2010.02.040

• Morphological correlates of MAO A VNTR polymorphism: New evidence from cortical thickness measurement, A. Cerasa, A. Cherubini, A. Quattrone, M.C. Gioia, A. Magariello, M. Muglia, I. Manna, F. Assogna, C. Caltagirone, G. Spalletta (2010). Behavioural Brain Research, in press 2010.

• The Role of the Fusiform-Amygdala System in the Pathophysiology of Autism, Dziobek, I., M. Bahnemann, A. Convit, H.R. Heekeren (2010). ARCH GEN PSYCHIATRY/VOL 67 (NO. 4), APR 2010.

• Phonetically irregular word pronunciation and cortical thickness in the adult brain, Karen Blackmon, William B.Barr, Ruben Kuzniecky, Jonathan DuBois, Chad Carlson, Brian T.Quinn, Mark Blumberg, Eric Halgren, Donald J. Hagler, Mark Mikhly, Orrin Devinsky, Carrie R. McDonald, Anders M. Dale, Thomas Thesen (2010). NeuroImage 51 (2010) 1453–1458

• Reduced right frontal cortical thickness in children, adolescents and adults with ADHD and its correlation to clinical variables: A cross-sectional study, Almeida, L.G., J. Ricardo-Garcell, H. Prado, L. Barajas, A. Fernández-Bouzas, D. Ávila, R.B. Martínez (2010). J. of Psychiatric Research, in press 2010.

• Amyloid-β Associated Cortical Thinning in Clinically Normal Elderly, J. Alex Becker, PhD, T. Hedden, PhD, J. Carmasin, BS, J. Maye, BS, D.M. Rentz, PsyD, D. Putcha, BA, B. Fischl, PhD, D. Greve, PhD, G. Marshall, MD, S. Salloway, MD, D. Marks, MD, R.L. Buckner, PhD, R.A. Sperling, MD and K.A. Johnson, MD (2010). Annals of Neurology, in press.

• Thickness of the human cerebral cortex is associated with metrics of cerebrovascular health in a normative sample of community dwelling older adults., Leritz EC, Salat DH, Williams VJ, Schnyer DM, Rudolph JL, Lipsitz L, Fischl B, McGlinchey RE, Milberg WP (2010). Neuroimage. 2010 Oct 28. [Epub ahead of print].

• Cortical thickness and subcortical volumes in schizophrenia and bipolar disorder, Rimol LM, Hartberg CB, Nesvåg R, Fennema-Notestine C, Hagler DJ Jr, Pung CJ, Jennings RG, Haukvik UK, Lange E, Nakstad PH, Melle I, Andreassen OA, Dale AM, Agartz I (2010). Biol Psychiatry. 2010 Jul 1;68(1):41-50.

• Cortical thickness is influenced by regionally specific genetic factors, Rimol LM, Panizzon MS, Fennema-Notestine C, Eyler LT, Fischl B, Franz CE, Hagler DJ, Lyons MJ, Neale MC, Pacheco J, Perry ME, Schmitt JE, Grant MD, Seidman LJ, Thermenos HW, Tsuang MT, Eisen SA, Kremen WS, Dale AM. Biol Psychiatry. 2010 Mar 1;67(5):493-9.

• Brain Structure in Young and Old East Asians and Westerners: Comparisons of Structural Volume and Cortical Thickness., Chee MW, Zheng H, Goh JO, Park D, Sutton BP (2010). J Cogn Neurosci. 2010 Apr 30.

• Dysbindin C–A–T haplotype is associated with thicker medial orbitofrontal cortex in healthy population, Antonio Cerasa, Aldo Quattrone, Maria C.Gioia, Patrizia Tarantino, Grazia Annesi, Francesca Assogna, Carlo Caltagirone, Vincenczo De Luca, Gianfranco Spalletta (2011). NeuroImage (2011), doi:10.1016/j.neuroimage.2010.12.042

• Patterns of cortical thinning in relation to event-based prospective memory performance three months after moderate to severe traumatic brain injury in children, McCauley, S.R., Wilde, E.A., Merkley, T.L., Schnelle, K.P., Bigler, E.D., Hunter, J.V., Chu, Z., Vasquez, A.C. and Levin, H.S. (2010). Dev Neuropsychol 35(3): 318-332.

• Amyloid-b Associated Cortical Thinning in Clinically Normal Elderly, Becker et al. (2010). Annals of Neurology, 2010 Nov 17.

• Reduced cortical thickness in the posterior cingulate gyrus is characteristic of both typical and atypical Alzheimer's disease. Lehmann, M. Rohrer, J.D., Clarkson, M.J., Ridgway, G.R., Scahill, R.I., Modat, M., Warren, J.D., Ourselin, S., Barnes, J., Rosser, M.N. and Fox, N.C. (2010) J Alzheimers Dis  20(2):587-98.

• Determining the optimal level of smoothing in cortical thickness analysis: a hierarchical approach based on sequential statistical thresholding. Bernal-Rusiel JL, Atienza M, Cantero JL (2010). Neuroimage, 52:158-171.

• Imaging derived cortical thickness reduction in high-functioning autism: Key regions and temporal slope, Christian Scheel, Anna Rotarska-Jagiela, Leonhard Schilbach, Fritz G. Lehnhardt, Barbara Krug, Kai Vogeley, and Ralf Tepes (2011). NeuroImage (in press).

• The Dynamics of Cortical and Hippocampal Atrophy in Alzheimer Disease, Sabuncu, M.R., R.S. Desikan, J. Sepulcre, B.T.T. Yeo, H. Liu, N.J. Schmansky, M. Reuter, M.W. Weiner, R.L. Buckner, R.A. Sperling, B. Fischl (2011). Archives of Neurology, Vol 68 (No. 8), Aug 2011. Supplemental

• Regional Cortical Thinning Associated with Detectable Levels of HIV DNA, Kallianpur KJ, Kirk GR, Sailasuta N, Valcour V, Shiramizu B, Nakamoto BK, Shikuma C (2011). Cereb Cortex. 2011 Oct 19.

• Cortical Thinning in Psychopathy, Martina Ly, Julian C. Motzkin, Carissa L. Philippi, Gregory R. Kirk, Joseph P. Newman, Kent A. Kiehl, Michael Koenigs. Am J Psychiatry. 2012 May 11.

• Distinct neuropsychological profiles correspond to distribution of cortical thinning in inherited prion disease caused be insertional mutation. Alner, K., Hyare, H., Mead, S., Rudge, P., Wroe, S., Rohrer, J.D., Ridgway, G.R., Ourselin, S., Clarkson, M. Hunt, H., Fox, N.C., Webb, T., Collinge, J. and Cipolotti, L.N. (2012) J Neurol Neurosurg Psychiatry 83(1):109-14.

• Focal cortical damage parallels cognitive impairment in minimal hepatic encephalopathy. Montoliu C, Gonzalez-Escamilla G, Atienza M, Urios A, Gonzalez O, Wassel A, Aliaga R, Giner-Duran R, Serra MA, Rodrigo JM, Belloch V, Felipo V, Cantero JL (2012). Neuroimage, 61:1165-1175.

• Sample size estimates for well-powered cross-sectional cortical thickness studies. Pardoe, H. R., Abbott, D. F., Jackson, G. D. and The Alzheimer's Disease Neuroimaging Initiative (2012), Hum. Brain Mapp.. doi: 10.1002/hbm.22120.

• A neurodevelopmental basis for BECTS: Evidence from structural MRI. Pardoe, H. R., Berg, A. T., Archer, J. S., Fulbright, R. K., and Jackson, G. D. (2013). Epilepsy Research. doi: 10.1016/j.eplepsyres.2012.11.008

• Sodium valproate use is associated with reduced parietal lobe thickness and brain volume. Pardoe, H. R., Berg, A. T., and Jackson, G. D. (2013). Neurology, 80 (20): 1895 - 1900. doi: 10.1212/WNL.0b013e318292a2e5

• Impact of regional cortical andsubcortical changes on processing speed in cerebral small vessel disease. Righart, R., Duering, M., Gonik, M., Jouvent, E., Reyes, S., Hervé, D., Chabriat, H., & Dichgans, M. (2013). Neuroimage: Clinical, In press. http://dx.doi.org/10.1016/j.nicl.2013.06.006

• Incident subcortical infarcts induce focal thinning in connected cortical areas. Duering, M., Righart, R., Csanadi, E., Jouvent, E., Hervé, D., Chabriat, H., Dichgans, M. (2012). Neurology, 79, 2025-2028

cortical surface area

• A common MECP2 haplotype associates with reduced cortical surface area in humans in two independent populations, Joyner AH, J CR, Bloss CS, Bakken TE, Rimol LM, Melle I, Agartz I, Djurovic S, Topol EJ, Schork NJ, Andreassen OA, Dale AM. Proc Natl Acad Sci U S A. 2009 Sep 8;106(36):15483-8.

• Candidate Gene Analysis of the Human Natural Killer-1 Carbohydrate Pathway and Perineuronal Nets in Schizophrenia: B3GAT2 Is Associated with Disease Risk and Cortical Surface Area, Kähler AK, Djurovic S, Rimol LM, Brown AA, Athanasiu L, Jönsson EG, Hansen T, Gústafsson O, Hall H, Giegling I, Muglia P, Cichon S, Rietschel M, Pietiläinen OP, Peltonen L, Bramon E, Collier D, Clair DS, Sigurdsson E, Petursson H, Rujescu D, Melle I, Werge T, Steen VM, Dale AM, Matthews RT, Agartz I, Andreassen OA (2010). Biol Psychiatry. 2010 Oct 14.

• Sex-dependent association of common variants of microcephaly genes with brain structure, Rimol LM, Agartz I, Djurovic S, Brown AA, Roddey JC, Kähler AK, Mattingsdal M, Athanasiu L, Joyner AH, Schork NJ, Halgren E, Sundet K, Melle I, Dale AM, Andreassen OA; Alzheimer's Disease Neuroimaging Initiative. Proc Natl Acad Sci U S A. 2010 Jan 5;107(1):384-8.

• Cortical volume, surface area, and thickness in schizophrenia and bipolar disorder. Rimol, L.M., Nesvag, R., Hagler, D.J., Jr., Bergmann, O., Fennema-Notestine, C., Hartberg, C.B., Haukvik, U.K., Lange, E., Pung, C.J., Server, A., Melle, I., Andreassen, O.A., Agartz, I., Dale, A.M. Biological Psychiatry. 2012 71, 552-560.

• Measuring and comparing brain cortical surface area and other areal quantities. Winkler AM, Sabuncu MR, Yeo BT, Fischl B, Greve DN, Kochunov P, Nichols TE, Blangero J, Glahn DC (2012). Neuroimage 61(4):1428-43.

local gyrification index (LGI)

• A Surface-Based Approach to Quantify Local Cortical Gyrification, Schaer, M., M. Bach Cuadra, L. Tamarit, F. Lazeyras, S. Eliez, and J.P. Thiran (2008). IEEE Transactions on Medical Imaging, Vol. 27, No. 2, February 2008. See also: JoVE video

• Congenital heart disease affects local gyrification in 22q11.2 deletion syndrome, Schaer, M., B. Glaser, M. Bach Cuadra, M. Debbané, J.-P. Thiran, S. Eliez (2009). Dev Med Child Neurol. 51(9):746-53.

• Decreased gyrification in major depressive disorder, Zhang Y, Yu C, Zhou Y, Li K, Li C, Jiang T. Neuroreport. 2009 Mar 4;20(4):378-80.

• Gyral and sulcal cortical thinning in adolescents with first episode early-onset psychosis, Janssen J, Reig S, Alemán Y, Schnack H, Udias JM, Parellada M, Graell M, Moreno D, Zabala A, Balaban E, Desco M, Arango C. Biol Psychiatry. 2009 Dec 1;66(11):1047-54. Epub 2009 Aug 31.

• Anomalous development of brain structure and function in spina bifida myelomeningocele, Juranek J, Salman MS. Dev Disabil Res Rev. 2010;16(1):23-30.

• Reduced cortical folding in mental retardation, Zhang Y, Zhou Y, Yu C, Lin L, Li C, Jiang T. AJNR Am J Neuroradiol. 2010 Jun;31(6):1063-7. Epub 2010 Jan 14.

• Cortical curvature analysis in MRI-negative temporal lobe epilepsy: a surrogate marker for malformations of cortical development, Ronan L, Scanlon C, Murphy K, Maguire S, Delanty N, Doherty CP, Fitzsimons M. Epilepsia. 2011 Jan;52(1):28-34. doi: 10.1111/j.1528-1167.2010.02895.x. Epub 2010 Dec 27.

• Folding of the prefrontal cortex in schizophrenia: regional differences in gyrification, Palaniyappan L, Mallikarjun P, Joseph V, White TP, Liddle PF. Biol Psychiatry. 2011 May 15;69(10):974-9. Epub 2011 Jan 22.

• Detection of epileptogenic cortical malformations with surface-based MRI morphometry, Thesen T, Quinn BT, Carlson C, Devinsky O, DuBois J, McDonald CR, French J, Leventer R, Felsovalyi O, Wang X, Halgren E, Kuzniecky R. PLoS One. 2011 Feb 4;6(2):e16430.

• Atypical developmental trajectory of functionally significant cortical areas in children with chromosome 22q11.2 deletion syndrome, Srivastava S, Buonocore MH, Simon TJ. Hum Brain Mapp. 2011 Mar 17. doi: 10.1002/hbm.21206

clinical biomarkers

• Temporoparietal MR Imaging Measures of Atrophy in Subjects with Mild Cognitive Impairment That Predict Subsequent Diagnosis of Alzheimer Disease, Desikan, R.S., H.J. Cabral, B. Fischl, C.R.G. Guttmann, D. Blacker, B.T. Hyman, M.S. Albert, R.J. Killiany (2009). AJNR American Journal of Neuroradiology;3:532-538.

• Automated MRI measures identify individuals with mild cognitive impairment and Alzheimer’s disease, Desikan, R.S., H.J. Cabral, C.P. Hess, W.P. Dillon, C.M. Glastonbury, M.W. Weiner, N.J. Schmansky, D.N. Greve, D.H. Salat, R.L. Buckner and B. Fischl (2009). Brain, 2009 May 21.

• Use of SVM Methods with Surface-Based Cortical and Volumetric Subcortical Measurements to Detect Alzheimer's Disease, Oliveira Jr., P.P.M., R. Nitrini, G. Busatto, C. Buchpiguel, J.R. Sato1, E. Amaro Jr. (2010). J of Alzheimer's Disease, 10.3233/JAD-2010-1322.

• Automated MRI measures predict progression to Alzheimer’s disease, Desikan R.S., H.J. Cabral, F. Settecase, C.P. Hess, W.P. Dillon, C.M. Glastonbury, M.W. Weiner, N.J. Schmansky, D.H. Salat, B. Fischl (2010). Neurobiology of Aging, 2010, Aug;31(8):1364-74.

• Describing the Brain in Autism in Five Dimensions — Magnetic Resonance Imaging-Assisted Diagnosis of Autism Spectrum Disorder Using a Multiparameter Classification Approach, Ecker, C., A. Marquand, J. Mourão-Miranda, P. Johnston, E.M. Daly, M.J. Brammer, S. Maltezos, C.M. Murphy, D. Robertson, S.C. Williams, and D.G.M. Murphy (2010). J. of Neuroscience, August 11, 2010 • 30(32):10612–10623.

• Selective Disruption of the Cerebral Neocortex in Alzheimer’s Disease, Desikan, R.S., M.R. Sabuncu, N.J. Schmansky, M. Reuter, H.J. Cabral, C.P. Hess, M.W. Weiner, A. Biffi, C.D. Anderson, J. Rosand, D.H. Salat, T.L. Kemper, A.M. Dale, R.A. Sperling, B. Fischl, the Alzheimer’s Disease Neuroimaging Initiative (2010). PLoS ONE 5(9): e12853.

• The Dynamics of Cortical and Hippocampal Atrophy in Alzheimer Disease, Sabuncu, M.R., R.S. Desikan, J. Sepulcre, B.T.T. Yeo, H. Liu, N.J. Schmansky, M. Reuter, M.W. Weiner, R.L. Buckner, R.A. Sperling, B. Fischl (2011). Archives of Neurology, Vol 68 (No. 8), Aug 2011. Supplemental

• Automatic classification of patients with Alzheimer's disease from structural MRI: A comparison of ten methods using the ADNI database, R Cuingnet, E Gerardin, J Tessieras, G Auzias. Neuroimage, 2011 - Elsevier.

volumetric

• Age does not increase rate of forgetting over weeks neuroanatomical volumes and visual memory across the adult life-span, Fjell, A.M., K.B. Walhovd, I. Reinvang, A. Lundervold, A.M. Dale, B.T. Quinn, N. Makris, and B. Fischl, (2005). Journal of the International Neuropsychological Society, 2-15(1):2-15.

• Cortical volume and speed-of-processing are complementary in prediction of performance intelligence, Walhovd, K.B., A.M. Fjell, I. Reinvang, A. Lundervold, B. Fischl, B.T. Quinn, N. Makris, and A.M. Dale, (2005). Neuropsychologia, 43(5):704-713.

• Effects of age on volumes of cortex, white matter and subcortical structures, Walhovd, K.B., A.M. Fjell, I. Reinvang, A. Lundervold, A.M. Dale, D.E. Eilertsen, B.T. Quinn, D. Salat, N. Makris, and B. Fischl (2005). Neurobiology of Aging 26:1261-1270. See also: Commentary: Neuroanatomical aging: Universal but not uniform.

• The functional and structural significance of the frontal shift in the old/new ERP effect, Walhovd, K.B., A.M. Fjell, I. Reinvang, A. Lundervold, B. Fischl, B.T. Quinn, N. Makris, and A.M. Dale, (2006). Brain Research, 1081:156-170.

• Interactive effects of APOE and CHRNA4 on attention and white matter volume in healthy middle-aged and older adults, Thomas Espeseth, Pamela M. Greenwood, Ivar Reinvang, Anders M. Fjell, Kristine B. Walhovd, Lars T. Westlye, Eike Wehling, Astri Lundervold, Helge Rootwelt, Raja Parasuraman. Cognitive, Affective, & Behavioral Neuroscience 2006, 6(1), 31-43.

• Detailed semiautomated MRI based morphometry of the neonatal brain: Preliminary results, Nishida, M., N. Makris, D.N. Kennedy, M. Vangel, B. Fischl, K.S. Krishnamoorthy, V.S. Caviness, and P.E. Grant (2007). NeuroImage 32:1041-1049.

• Volumetric cerebral characteristics of children exposed to opiates and other substances in utero, Walhovd, K.B., V. Moe, K. Slinning, P. Due-Tønnessen, A. Bjørnerud, A.M. Dale, A. van der Kouwe, B.T. Quinn, B. Kosofsky, D. Greve, and B. Fischl, (2007). NeuroImage 36:1331-1344.

• White matter volume predicts reaction time instability, Kristine B. Walhovd , Anders M. Fjell. Neuropsychologia 45 (2007) 2277–2284.

• Feasibility of Multi-site Clinical Structural Neuroimaging Studies of Aging Using Legacy Data, Fennema-Notestine, C., A.C. Gamst, B.T. Quinn, J. Pacheco, T.L. Jernigan, L. Thal, R. Buckner, R. Killiany, D. Blacker, A.M. Dale, B. Fischl, B. Dickerson, R.L. Gollub, (2007). Neuroinformatics 5:235-245.

• The Effect of Early Human Diet on Caudate Volumes and IQ, Isaacs, E.B., D.G. Gadian, S. Sabatini, W.K. Chong, B.T. Quinn, B.R. Fischl, and A. Lucas, (2008). Pediatric Research 63(3):308-314. (see also: commentary)

• Subcortical and cerebellar atrophy in mesial temporal lobe epilepsy revealed by automatic segmentation, McDonald, C.R., D.J. Hagler, Jr., M.E. Ahmadi, E. Tecoma, V. Iragui, A.M. Dale, and E. Halgren (2008). Epilepsy Researc 2008 Mar 20.

• Heritability of Brain Morphology Related to Schizophrenia: A Large-Scale Automated Magnetic Resonance Imaging Segmentation Study, Goldman, A.L., L. Pezawas, V.S. Mattay, B. Fischl, B.A. Verchinski, B. Zoltick, D.R. Weinberger, and A. Meyer-Lindenberg (2008). Biological Psychiatry 2008 63:475–483.

• Cerebellar Atrophy in Essential Tremor Using an Automated Segmentation Method, A.Cerasa, D.Messina, G.Nicoletti, F.Novellino, P.Lanza, F.Condino, G.Arabia, M.Salsone, A.Quattrone (2009). AJNR 2009 Published April 2, 2009.

• The COMT Val108/158Met polymorphism and medial temporal lobe volumetry in patients with schizophrenia and healthy adults, Ehrlich, S., E.M. Morrow, J.L. Roffman, S.R. Wallace, M. Naylore, H.J. Bockholt, A. Lundquist, A. Yendiki, B.C. Ho, T. White, D.S. Manoach, V.P. Clark, V.D. Calhoun, R.L. Gollub and D.J. Holt (2009). Neuroimage. 2009 Dec 21.

• Smaller global and regional cortical volume in combat-related posttraumatic stress disorder, Woodward, S.H., M. Schaer, D. G. Kaloupek, L. Cediel, S. Eliez (2009). Arch Gen Psychiatry. 66(12):1373-82.

• Regional cortical volumes and congenital heart disease: a MRI study in 22q11.2 deletion syndrome, Schaer, M., B. Glaser, M.-C. Ottet, M. Schneider, M. Bach Cuadra, M. Debbané, J.-P. Thiran, S. Eliez (2010). J Neurodevep Disord. DOI10.1007/s11689-010-9061-4.

• Testosterone modifies the effect of APOE genotype on hippocampal volume in middle-aged men, M.S. Panizzon, R. Hauger, A.M. Dale, L.J. Eaves, L.T. Eyler, B. Fischl, C. Fennema-Notestine, C.E. Franz, M.D. Grant, A.J. Jak, K.C. Jacobson, M.J. Lyons, S.P. Mendoza, M.C. Neale, E.C. Prom-Wormley, L.J. Seidman, M.T. Tsuang, H. Xian and W.S. Kremen (2010). 2010;75;874-880Neurology. DOI: 10.1212/WNL.0b013e3181f11deb

• Gray matter volume reduction in rostral middle frontal gyrus in patients with chronic schizophrenia, Z.Kikinis, J.H.Fallon, M.Niznikiewicz, P.Nestor, C.Davidson, L.Bobrow, P.E.Pelavin, B.Fischl, A.Yendiki, R.W.McCarley, R.Kikinis, M.Kubicki, M.E.Shenton (2010). Schizophrenia Research 123 (2010)153–159.

• Cortical thickness and subcortical volumes in schizophrenia and bipolar disorder, Rimol LM, Hartberg CB, Nesvåg R, Fennema-Notestine C, Hagler DJ Jr, Pung CJ, Jennings RG, Haukvik UK, Lange E, Nakstad PH, Melle I, Andreassen OA, Dale AM, Agartz I (2010). Biol Psychiatry. 2010 Jul 1;68(1):41-50.

• Sex-dependent association of common variants of microcephaly genes with brain structure, Rimol LM, Agartz I, Djurovic S, Brown AA, Roddey JC, Kähler AK, Mattingsdal M, Athanasiu L, Joyner AH, Schork NJ, Halgren E, Sundet K, Melle I, Dale AM, Andreassen OA; Alzheimer's Disease Neuroimaging Initiative. Proc Natl Acad Sci U S A. 2010 Jan 5;107(1):384-8.

• MAO A VNTR polymorphism and amygdala volume in healthy subjects, Antonio Cerasa, Aldo Quattrone, Maria C.Gioia, Angela Magariello, Maria Muglia, Francesca Assogna, Sergio Bernardini, Carlo Caltagirone, Paola Bossu, Gianfranco Spalletta (2011). Neuroimaging (2011), doi:10.1016/j.pscychresns.2010.11.002

• Patterns of brain atrophy in Parkinson’s disease, progressive supranuclear palsy and multiple system atrophy, Demetrio Messina, Antonio Cerasa, Francesca Condino, Gennarina Arabia, Fabiana Novellino, Giuseppe Nicoletti, Maria Salsone, Maurizio Morelli, Pier Luigi Lanza, Aldo Quattrone (2011). Parkinsonism and Related Disorders (2011), doi:10.1016/j.parkreldis.2010.12.010

• The Dynamics of Cortical and Hippocampal Atrophy in Alzheimer Disease, Sabuncu, M.R., R.S. Desikan, J. Sepulcre, B.T.T. Yeo, H. Liu, N.J. Schmansky, M. Reuter, M.W. Weiner, R.L. Buckner, R.A. Sperling, B. Fischl (2011). Archives of Neurology, Vol 68 (No. 8), Aug 2011. Supplemental

• Genetic influences on hippocampal volume differ as a function of testoterone level in middle-aged men, Matthew S. Panizzon, Richard L. Hauger, Lindon J. Eaves, Chi-Hua Chen, Anders M. Dale, Lisa T. Eyler, Bruce Fischl, Christine Fennema-Notestine, Carol E. Franz, Michael D. Grant, Kristen C. Jacobson, Amy J. Jak, Michael J. Lyons, Sally P. Mendoza, Michael C. Neale, Elizabeth Prom-Wormley, Larry J. Seidman, Ming T. Tsuang, Hong Xian, William S. Kremen (2011). doi:10.1016/j.neuroimage.2011.09.044

• Clinical and neuroanatomical signatures of tissue pathology in frontotemporal lobar degeneration. Rohrer, J. D., Lashley, T. Schott, J.M., Warren J.E., Mead, S. Isaacs, A.M., Beck, J., Hardy, J., de Silva, R., Warrington E., Troakes, C., Al-Sarraj, S., King, A., Barroni, B., Clarkson, M.J., Ourselin, S., Holton, J.L., Fox, N.C., Revesc, T., Rosser, M.N. and Warren J. D. (2011) Brain 134(Pt 9):2565-81

• Cognitive reserve moderates the association between hippocampal volume and episodic memory in middle age, Vuoksimaa, E., Panizzon, M., Chen, C., Eyler, L., Fennema-Notestine, C., Fiecas, M., Fischl, B., Franz, C., Grant, M., Jak, A., Lyons, M., Neale, M., Thompson, W., Tsuang, M., Xian, H., Dale, A., Kremen, W. 2013 Neuropsychologia 51:1124-1131

white matter

• Regional white matter volume differences in nondemented aging and Alzheimer's disease, Salat D.H., D.N. Greve, J.L. Pacheco, B.T. Quinn, K.G. Helmer, R.L. Buckner, B. Fischl (2008). NeuroImage 44 (2009) 1247–1258.

• Impact of breast milk on IQ, brain size and white matter development, Elizabeth B. Isaacs, Bruce R. Fischl, Brian T. Quinn, Wui K. Chong, David G. Gadian, and Alan Lucas. (2009). Pediatric Research Accepted Manuscript.

longitudinal

• MRI measures of temporoparietal regions show differential rates of atrophy during prodromal AD, Desikan, R.S., B. Fischl, H.J. Cabral, T.L. Kemper, C.R.G. Guttmann, D. Blacker, B.T. Hyman, M.S. Albert, R.J. Killiany, (2008). Neurology 2008, doi:10.1212/01.wnl.0000320055.57329.34.

• Deviant trajectories of cortical maturation in 22q11.2 deletion syndrome (22q11DS): a cross-sectional and longitudinal study, Schaer, M., M. Debbané, M. Bach Cuadra, M.-C. Ottet, B. Glaser, J.-P. Thiran, S. Eliez (2009) Schizophr Res. 115(2-3):182-90.

• Effects of memory training on cortical thickness in the elderly, Engvig A, Fjell AM, Westlye LT, Moberget T, Sundseth Ø, Larsen VA, Walhovd KB (2010). Neuroimage. 2010 Oct 1;52(4):1667-76.

• The Dynamics of Cortical and Hippocampal Atrophy in Alzheimer Disease, Sabuncu, M.R., R.S. Desikan, J. Sepulcre, B.T.T. Yeo, H. Liu, N.J. Schmansky, M. Reuter, M.W. Weiner, R.L. Buckner, R.A. Sperling, B. Fischl (2011). Archives of Neurology, Vol 68 (No. 8), Aug 2011. Supplemental

cortical region localization

• Detection of entorhinal layer II using 7 Tesla magnetic resonance imaging, Augustinack, Jean C., Andre J. W. van der Kouwe, Megan L. Blackwell, David H. Salat, Christopher J. Wiggins, Matthew P. Frosch, Graham C. Wiggins, Andreas Potthast, Lawrence L. Wald, Bruce R. Fischl, (2005). Annals of Neurology, 57(4):489-494.

• Predicting the location of entorhinal cortex from MRI, B. Fischl, A. A. Stevens, N. Rajendran, B. T. T.Yeo, D. N. Greve, K. V. Leemput, J. R. Polimeni, S. Kakunoori, R. L. Buckner, J. Pacheco, D. H. Salat, J. Melcher, M. P. Frosch, B. T. Hyman, P. E. Grant, B. R. Rosen, A. J.W. van der Kouwe, G. C. Wiggins, L. L. Wald, J. C. Augustinack, (2009). NeuroImage (2009).

• Predicting the location of human perirhinal cortex, Brodmann's area 35, from MRI, Augustinack JC, Huber KE, Stevens AA, Roy M, Frosch MP, van der Kouwe AJW, Wald LL, Van Leemput K, McKee AC, Fischl B. NeuroImage 64(2013), 32-42.

cortical surface shape and folding analysis

• Cortical Surface Shape Analysis Based on Spherical Wavelets, Yu, P., P.E. Grant, Y. Qi, X. Han, F. Ségonne, R. Pienaar, E. Busa, J. Pacheco, N. Makris, R.L. Buckner, P. Golland, and B. Fischl (2007). IEEE Transactions on Medical Imaging, 26(4):582-597.

• Cortical folding development study based on over-complete spherical wavelets Yu, P., B.T.T. Yeo, P.E. Grant, B. Fischl, P. Golland (2007). Proceedings of the IEEE International Conference on Computer Vision (MMBIA 2007).

• Abnormal cortical folding patterns within Broca's area in schizophrenia: Evidence from structural MRI, Wisco, J.J., G. Kuperberg, D. Manoach, B.T. Quinn, E. Busa, B. Fischl, S. Heckers, A.G. Sorensen (2007). Schizophrenia Research, 94(1-3):317-327.

• A Methodology for Analyzing Curvature in the Developing Brain from Preterm to Adult, R.Pienaar, B.Fischl, B.Caviness, N.Makris, P.E.Grant. (2008) International Journal of Imaging Systems and Technology Special Issue: Human Brain Imaging, 18(1): 42-68.

• Shape Analysis with Overcomplete Spherical Wavelets B.T.T. Yeo, P. Yu, P.E. Grant, B. Fischl, P. Golland. Proceedings of the International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), volume 5241 of LNCS, 468--476, 2008

• Does Retinotopy Influence Cortical Folding in Primate Visual Cortex?, Reza Rajimehr, Roger B.H.Tootell (2009). The Journal of Neuroscience, September 9, 2009 • 29(36):11149 –11152.

• Congenital heart disease affects local gyrification in 22q11.2 deletion syndrome, Schaer, M., B. Glaser, M. Bach Cuadra, M. Debbané, J.-P. Thiran, S. Eliez (2009). Dev Med Child Neurol. 51(9):746-53.

• Dreidimensionale zeitauflösende Untersuchung der kortikalen Faltungsstruktur am Beispiel der Schizophrenie, Burkhard Metten. Der Andere Verlag Tönning, Lübeck, Marburg (2010). ISBN 978-3-86247-057-0 [in German]

• Intrinsic Curvature: A Marker Of Millimeter-Scale Tangential Cortico-Cortical Connectivity?, Lisa Ronan, Rudolph Pienaar, Guy Williams, Ed Bullmore, Tim J. Crow, Neil Roberts, Peter B. Jones, John Suckling, Paul C. Fletcher (2011). International Journal of Neural Systems, Vol. 21, No. 5 (2011) 351–366

surface-based analysis (SBA)

• A human parietal face area contains aligned head-centered visual and tactile maps, Sereno, M.I. and RS Huang, (2006). Nature Neuroscience 9:1337-1343.

• Enhanced Cortical Activation in the Contralesional Hemisphere of Chronic Stroke Patients in Response to Motor Skill Challenge, Schaechter, J.D., and K.L. Perdue (2007). Cerebral Cortex, 2007 Jun 29 [Epub ahead of print].

• Smoothing and cluster thresholding for cortical surface-based group analysis of fMRI data, Hagler Jr., D.J., A. Pinar Saygin, and M.I. Sereno. NeuroImage (2006), doi:10.1016/j.neuroimage.2006.07.036.

• Laminar analysis of 7T BOLD using an imposed spatial activation pattern in human V1., Polimeni JR, Fischl B, Greve DN, Wald LL. Neuroimage. 2010 Oct 1;52(4):1334-46.

• The Minimal Preprocessing Pipelines for the Human Connectome Project, Glasser, MF, Sotiropoulos, SN, Wilson, JA, Coalson, TS, Fischl B, Andersson, JL, Xu, J, Jbabdi, S, Webster, M, Polimeni, JR, Van Essen, DC, Jenkinson, M, WU-Minn HCP Consortium. Neuroimage. 2013, in press.

ROI-based analysis

• Effects of mindful-attention and compassion meditation training on amygdala response to emotional stimuli in an ordinary, non-meditative state, Desbordes, G., Negi, L.T., Pace T.W.W., Wallace, B.A., Raison, C.L., Schwartz, E.L. Frontiers in Human Neuroscience. 2012. 6:292. doi: 10.3389/fnhum.2012.00292.

SBA vs. VBM

• Evidence for abnormalities of cortical development in Adolescent-Onset Schizophrenia, Voets, N.L., M. Hough, G. Douaud, P.M. Matthews, A. James, L. Winmill, P. Webster, S. Smith (2008). NeuroImage, doi: 10.1016/j.neuroimage.2008.08.013.

• Cortical thickness or grey matter volume? The importance of selecting the phenotype for imaging genetics studies, A.M. Winkler, P.Kochunov, J.Blangero, L.Almasy, K.Zilles,. P.T. Fox, R.Duggirala and D.C. Glahn (2009). doi:10.1016/j.neuroimage.2009.12.028

• Dysbindin C–A–T haplotype is associated with thicker medial orbitofrontal cortex in healthy population, Antonio Cerasa, Aldo Quattrone, Maria C.Gioia, Patrizia Tarantino, Grazia Annesi, Francesca Assogna, Carlo Caltagirone, Vincenczo De Luca, Gianfranco Spalletta (2011). NeuroImage (2011), doi:10.1016/j.neuroimage.2010.12.042

• Brain Structure in Young and Old East Asians and Westerners: Comparisons of Structural Volume and Cortical Thickness., Chee MW, Zheng H, Goh JO, Park D, Sutton BP (2010). J Cogn Neurosci. 2010 Apr 30.

diffusion analysis

• The relationship between diffusion tensor imaging and volumetry as measures of white matter properties, Anders M Fjell, Lars T Westlye, Doug N. Greve, Bruce Fischl, Thomas Benner, André J. W. van der Kouwe, David Salat, Atle Bjørnerud, Paulina Due-Tønnessen, Kristine B Walhovd. NeuroImage, in press.

• White matter pathology isolates the hippocampal formation in Alzheimer's disease, D.H. Salat, D.S. Tuch, A.J.W. van der Kouwe, D.N. Greve, V. Pappu, S.Y. Lee, N.D. Hevelone, A.K. Zaleta, J.H. Growdon, S. Corkin, B. Fischl, H.D. Rosas. Neurobiology of Aging 31 (2010) 244–256

• Improved Tractography Alignment Using Combined Volumetric and Surface Registration, Lilla Zollei, Allison Stevens, Kristen Huber, Sita Kakunoori, Bruce Fischl ( 2010). doi:10.1016/j.neuroimage.2010.01.101

• Direct visualization of the perforant pathway in the human brain with ex vivo diffusion tensor imaging, Jean C. Augustinack, Karl Helmer, Kristen E. Huber, Sita Kakunoori, Lilla Zöllei and Bruce Fischl (2010). Frontiers in Human Neuroscience, May 2010 | Volume 4 | Article 42.

• Probing brain connectivity by combined analysis of diffusion MRI tractography and electrocorticography, Kathrin Tertel, Nitin Tandon, Timothy M.Ellmore (2010). Comput. Biol. Med. (2010), doi:10.1016/j.compbiomed.2010.11.004

• Connectivity-based segmentation of human amygdala nuclei using probabilistic tractography, Zeynep M. Saygin, David E. Osher, Jean Augustinack, Bruce Fischl, John D.E. Gabrieli. NeuroImage 56 (2011) 1353-1361.

• Radial and tangential neuronal migration pathways in the human fetal brain: Anatomically distinct patterns of diffusion MRI coherence, James Kolasinski, Emi Takahashi, Allison A. Stevens, Thomas Benner, Bruce Fischl, Lilla Zöllei, P. Ellen Grant. NeuroImage 79 (2013) 412-422. doi: 10.1016/j.neuroimage.2013.04.125

CBF - cerebral blood flow

• Age-associated reductions in cerebral blood flow are independent from regional atrophy, J. Jean Chen, H. Diana Rosas, David H. Salat (2011). NeuroImage 55 (2011) 468–478.

cortical flat-patches

• Attentional modulation of human auditory cortex, Petkov, C.I., X. Kang, K. Alho, O. Bertrand, W.E. Yund, and D.L. Woods, (2004). Nature Neuroscience 7:658-663.

FS-FAST

• Faces and objects in macaque cerebral cortex, Tsao, D.Y., W.A. Freiwald, T.A. Knutsen, J.B. Mandeville and R.B.H. Tootell, (2003). Nature Neuroscience 6:989-995.

validation / evaluation

• Quantitative evaluation of three cortical surface flattening methods Ju, L., M.K. Hurdal, J. Stern, K. Rehm, K. Schaper, and D. Rottenberg (2005). NeuroImage 28 (2005) 869 – 880.

• A novel quantitative cross-validation of different cortical surface reconstruction algorithms using MRI phantom, Lee, J.K., J.M. Lee, J.S. Kim, I.Y. Kim, A.C. Evans, and S.I. Kim (2006). NeuroImage 31 (2006) 572 – 584.

• Comparative Reliability of Total Intracranial Volume Estimation Methods and the Influence of Atrophy in a Longitudinal Semantic Dementia Cohort, Pengas, G., J.M.S. Pereira, G.B. Williams, P.J. Nesto (2008). J. Neuroimaging 2008;XX:1-10.

• Validation of hippocampal volumes measured using a manual method and two automated methods (FreeSurfer and IBASPM) in chronic major depressive disorder, Tae, W.S, S.S. Kim, K.U. Lee, E.C. Nam, and K.W. Kim (2008). Neuroradiology DOI 10.1007/s00234-008-0383-9.

• In Vivo Hippocampal Measurement and Memory: A Comparison of Manual Tracing and Automated Segmentation in a Large Community-Based Sample, Cherbuin, N., K.J. Anstey, C. Re´glade-Meslin, P.S. Sachdev (2009). PLoS ONE 4(4): e5265. doi:10.1371/journal.pone.0005265.

• A comparison of automated segmentation and manual tracing for quantifying hippocampal and amygdala volumes, Morey, R.A., C.M. Petty, Y. Xu, J. Pannu Hayes, H.R. Wagner II, D.V. Lewis, K.S. LaBar, M. Styner, G. McCarthy (2009). NeuroImage, article-in-press.

• Hippocampal volume assessment in temporal lobe epilepsy: How good is automated segmentation?, Pardoe HR, Pell GS, Abbott DF, Jackson GD (2009). Epilepsia. 2009 Dec;50(12):2586-92.

• Comparison of landmark-based and automatic methods for cortical surface registration, Pantazis D., A. Joshi, J. Jiang, D. Shattuck, L.E. Bernstein, H. Damasio, R.M. Leahy (2009). Neuroimage, 2010 Feb 1;49(3):2479-93.

• Evaluation of volume-based and surface-based brain image registration methods., Arno Klein, Satrajit S. Ghosh, Brian Avants, B.T.T. Yeo, Bruce Fischl, Babak Ardekani, James C. Gee, J.J. Mann, Ramin V. Parsey. (2010). NeuroImage. doi:10.1016/j.neuroimage.2010.01.091

• Comparison of Manual and Automated Determination of Hippocampal Volumes in MCI and Early AD, Li Shen, Andrew J. Saykin, Sungeun Kim, Hiram A. Firpi, John D. West, Shannon L. Risacher, Brenna C. McDonald, Tara L. McHugh, Heather A. Wishart, Laura A. Flashman (2010). Brain Imaging and Behavior (2010) 4:86–95. DOI 10.1007/s11682-010-9088-x.

• Reliability and validity of MRI-based automated volumetry software relative to auto-assisted manual measurement of subcortical structures in HIV-infected patients from a multisite study, Dewey J, Hana G, Russell T, Price J, McCaffrey D, Harezlak J, Sem E, Anyanwu JC, Guttmann CR, Navia B, Cohen R, Tate DF; HIV Neuroimaging Consortium (2010). Neuroimage. 2010 Jul 15;51(4):1334-44.

• Quantitative evaluation of LDDMM, FreeSurfer, and CARET for cortical surface mapping, Zhong J, Phua DY, Qiu A (2010). Neuroimage, 2010 Aug 1;52(1):131-41.

• Diffuse damage in pediatric traumatic brain injury: a comparison of automated versus operator-controlled quantification methods, Bigler, E.D, Abildskov, T.J., Wilde, E.A., McCauley, S.R,Li, X., Merkley, T.L., Fearing, M.A., Newsome, M.R., Scheibel, R.S., Hunter, J.V., Chu, Z. and Levin, H.S. (2010). Neuroimage 50(3): 1017-1026.

• Manual validation of FreeSurfer's automated hippocampal segmentation in normal aging, mild cognitive impairment, and Alzheimer Disease subjects, Sanchez-Benavides, G., Gomez-Anson, B., Sainz, A., Vives, Y., Delfino, M. and Pena-Casanova, J. (2010). Psychiatry Res 181(3): 219-225.

• Evaluating the validity of volume-based and surface-based brain image registration for developmental cognitive neuroscience studies in children 4 to 11 years of age., Satrajit S. Ghosh, Sita Kakunoori, Jean Augustinack, Alfonso Nieto-Castanon, Ioulia Kovelman, Nadine Gaab, Joanna A. Christodoulou, Christina Triantafyllou, John D.E. Gabrieli, Bruce Fischl (2010). NeuroImage 53 (2010) 85–93

• Head size, age and gender adjustment in MRI studies: a necessary nuisance?. Barnes, J., Ridgway, G.R., Barlett, J., Henley, S.M., Lehmann, M., Hobbs, N., Clarkson, M.J., MacManus, D.G., Ourselin S. and Fox, N.C. (2010) Neuroimage 53(4):1244-55

• Scan–rescan reliability of subcortical brain volumes derived from automated segmentation. Morey, R. A., Selgrade, E. S., Wagner, H. R., Huettel, S. A., Wang, L. and McCarthy, G. (2010) Hum. Brain Mapp., 31: 1751–1762.

• Automatic classification of patients with Alzheimer's disease from structural MRI: A comparison of ten methods using the ADNI database, R Cuingnet, E Gerardin, J Tessieras, G Auzias. Neuroimage, 2011 - Elsevier.

• A comparison of voxel and surface based cortical thickness estimation methods. Clarkson, M.J., Cardoso, M.J., Ridgway, G.R., Modat, M., Leung, K.K., Rohrer, J.D., Fox, N.C. and Ourselin, S. (2011) Neuroimage 57(3):856-65

• Automatic hippocampal segmentation in temporal lobe epilepsy: impact of developmental abnormalities, Kim H, Chupin M, Colliot O, Bernhardt BC, Bernasconi N, Bernasconi A. (2011). Neuroimage. 2012 Feb 15;59(4):3178-86.

• Volume Estimation of the Thalamus Using Freesurfer and Stereology: Consistency between Methods., Keller SS, Gerdes JS, Mohammadi S, Kellinghaus C, Kugel H, Deppe K, Ringelstein EB, Evers S, Schwindt W, Deppe M. (2012). Neuroinformatics. 2012 Apr 6.

• The Effects of FreeSurfer Version, Workstation Type, and Macintosh Operating System Version on Anatomical Volume and Cortical Thickness Measurements, Gronenschild EHBM, Habets P, Jacobs HIL, Mengelers R, Rozendaal N, et al. (2012). PLoS ONE 7(6): e38234. doi:10.1371/journal.pone.0038234