Published material describing the techniques used in FreeSurfer ([http://www.nmr.mgh.harvard.edu/martinos/userInfo/data/cite.php please cite our software!]):

• surface reconstruction:

  • [https://surfer.nmr.mgh.harvard.edu/ftp/articles/dale99-recon1.pdf Cortical Surface-Based Analysis I: Segmentation and Surface Reconstruction], Dale, A.M., Fischl, B., Sereno, M.I., (1999). NeuroImage 9(2):179-194

  • [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl99b-recon2.pdf 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.

  • [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl01-topology-fixing.pdf 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.

  • [https://surfer.nmr.mgh.harvard.edu/ftp/articles/dalesereno93-ms.pdf 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.

  • [http://www.nmr.mgh.harvard.edu/~fischl/reprints/Neuroimage_Segonne_watershed.pdf 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.

  • [http://www.nmr.mgh.harvard.edu/~fischl/reprints/segonne_ga_ipmi2005.pdf Genetic Algorithm for the Topology Correction of Cortical Surfaces], F. Segonne, E. Grimson, B. Fischl (2005). IPMI pp393--405.

• inter-subject spherical averaging:

  • [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl99-morphing.pdf 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).

• thickness measurement:

  • [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl00-cortical-thickness.pdf 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.

  • [http://www.nmr.mgh.harvard.edu/~fischl/reprints/Han_NeuroImage_2006_thickness_reliability.pdf 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:

  • [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl04-parcellation.pdf 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.

  • [https://surfer.nmr.mgh.harvard.edu/ftp/articles/desikan06-parcellation.pdf 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.

  • [https://surfer.nmr.mgh.harvard.edu/ftp/articles/ba_maps2007.pdf Cortical Folding Patterns and Predicting Cytoarchitecture], Fischl, B., N. Rajendran, E. Busa, J. Augustinack, O. Hinds, B.T.T. Yeo, H. Mohlberg, K. Amunts, K. Zilles, (2007). Cerebral Cortex 2007, doi:10.1093/cercor/bhm225.

• subcortical segmentation:

  • [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl02-labeling.pdf 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.

  • [http://www.nmr.mgh.harvard.edu/~fischl/reprints/sequence_independent_segmentation_reprint.pdf 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.

  • [https://surfer.nmr.mgh.harvard.edu/ftp/articles/AtlasSeg_TMI2007April.pdf 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.

• related methodological papers

  • [http://www.nmr.mgh.harvard.edu/~fischl/reprints/Golland_MICCAI2002.pdf 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.

  • [http://www.nmr.mgh.harvard.edu/~fischl/reprints/golland-fischl-ipmi03.pdf 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.

  • [http://www.nmr.mgh.harvard.edu/~fischl/reprints/segonne_subcortical_topology_miccai2003.pdf Topology Correction of Subcortical Segmentation], Segonne, F., E. Grimson and B. Fischl, (2003) MICCAI 2003.

  • [https://surfer.nmr.mgh.harvard.edu/ftp/articles/jovicich_neuroimage_2006.pdf 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.

  • [https://surfer.nmr.mgh.harvard.edu/ftp/articles/IEEE.TMI.segonne.2007.separating.loops.pdf 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.

  • [https://surfer.nmr.mgh.harvard.edu/ftp/articles/PNAS-07-04515.pdf Phase maps reveal cortical architecture], Bruce Fischl and Lawrence L. Wald, PNAS, July 10, 2007, vol. 104, no. 28.

  • [https://surfer.nmr.mgh.harvard.edu/ftp/articles/yeo_MICCAI_2007.pdf Effects of Registration Regularization and Atlas Sharpness on Segmentation Accuracy], Yeo, B.T.T., M. Sabuncu, R. Desikan, B. Fischl, P. Golland (2007). Proceedings of the International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2007).

  • [https://surfer.nmr.mgh.harvard.edu/ftp/articles/yeo_MMBIA_2007.pdf 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).

  • [https://surfer.nmr.mgh.harvard.edu/ftp/articles/Bischoff-Grethe2007.pdf 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.

  • [https://surfer.nmr.mgh.harvard.edu/pub/articles/dickerson2007_methods.pdf 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.

Published material citing Freesurfer:

• cortical thickness

  • [http://www.nmr.mgh.harvard.edu/~fischl/reprints/hd_neurology_reprint.pdf 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.

  • [http://www.nmr.mgh.harvard.edu/~fischl/reprints/Kuperberg_and_Fischl_ArchGenPsy_03.pdf 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.

  • [http://www.nmr.mgh.harvard.edu/~fischl/reprints/Brain2003v126p1734Sailercorticalthickness.pdf 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. ([http://www.nmr.mgh.harvard.edu/~fischl/reprints/Brain2003v126p1719editorialMatthewscortex.pdf See also: editorial])

  • [https://surfer.nmr.mgh.harvard.edu/ftp/articles/salat04-thinning.pdf 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.

  • [http://www.nmr.mgh.harvard.edu/~fischl/reprints/rauch_2004_reprint.pdf 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.

  • [http://www.nmr.mgh.harvard.edu/~fischl/reprints/BrianGoldSemantifDementaNeuropsychologia_43.pdf 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.

  • [https://surfer.nmr.mgh.harvard.edu/pub/articles/Milad_et_al_PNAS_2005.pdf 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.

  • [https://surfer.nmr.mgh.harvard.edu/pub/articles/Lazar_Meditation_Plasticity_05.pdf 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.

  • [https://surfer.nmr.mgh.harvard.edu/pub/articles/fjell2006a.pdf 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.

  • [https://surfer.nmr.mgh.harvard.edu/pub/articles/walhovd2006b.pdf 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.

  • [https://surfer.nmr.mgh.harvard.edu/pub/articles/Sigalovsky_et_al_2006.pdf 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.

  • [https://surfer.nmr.mgh.harvard.edu/pub/articles/hadjikhani_ccortex_2006.pdf 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.

  • [https://surfer.nmr.mgh.harvard.edu/pub/articles/brain.2007.du_weiner.AD.thickness.pdf 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.

  • [https://surfer.nmr.mgh.harvard.edu/pub/articles/dickerson_nbiolaging_inpress_2007.pdf 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.

  • [https://surfer.nmr.mgh.harvard.edu/pub/articles/DaSilva_alNeurology2007.pdf 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.

  • [https://surfer.nmr.mgh.harvard.edu/pub/articles/Dickerson-NeuroImage2008.pdf 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.

  • 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, E. Halgren (2008). Epilepsia. 2008 Feb 7.

• volumetric

  • [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fjell2005.pdf 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.

  • [https://surfer.nmr.mgh.harvard.edu/ftp/articles/walhovd2005.pdf 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.

  • [https://surfer.nmr.mgh.harvard.edu/pub/articles/walhovd2005a.pdf 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: [https://surfer.nmr.mgh.harvard.edu/pub/articles/walhovd2005b.pdf Commentary: Neuroanatomical aging: Universal but not uniform].

  • [https://surfer.nmr.mgh.harvard.edu/ftp/articles/walhovd2006a.pdf 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.

  • [https://surfer.nmr.mgh.harvard.edu/ftp/articles/neonatal_morphometry.pdf 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.

  • [https://surfer.nmr.mgh.harvard.edu/ftp/articles/Walhovd_Neuroimage_2007.pdf 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.

  • [https://surfer.nmr.mgh.harvard.edu/ftp/articles/Neuroinformatics2007.pdf 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.

• entorhinal cortex

  • [http://www.nmr.mgh.harvard.edu/~fischl/reprints/EC_islands_annals_of_neurology_reprint.pdf 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.

• cortical surface shape and folding analysis

  • [https://surfer.nmr.mgh.harvard.edu/ftp/articles/yu_tmi_0704.pdf 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.

  • [https://surfer.nmr.mgh.harvard.edu/ftp/articles/yu_MMBIA_2007.pdf 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).

  • [https://surfer.nmr.mgh.harvard.edu/ftp/articles/Wisco_Sorensen_SzRes_07.pdf 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.

  • [https://surfer.nmr.mgh.harvard.edu/ftp/articles/hinds2007accurate.pdf 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 (2007). NeuroImage 2007.10.033.

• surface-based analysis

  • [http://www.nature.com/neuro/journal/v9/n10/full/nn1777.html 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.

  • [https://surfer.nmr.mgh.harvard.edu/ftp/articles/Schaechter_CC_2007.pdf 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].

• cortical flat-patches

  • [http://www.nature.com/neuro/journal/v7/n6/full/nn1256.html 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

  • [http://www.nature.com/neuro/journal/v6/n9/full/nn1111.html 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.