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| Articles describing the techniques used in FreeSurfer: | Published material describing the techniques used in !FreeSurfer ([http://www.nmr.mgh.harvard.edu/martinos/userInfo/data/cite.php please cite our software!]): |
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| 1. [http://surfer.nmr.mgh.harvard.edu/ftp/articles/dale99-recon1.pdf Cortical Surface-Based Analysis I: Segmentation and Surface Reconstruction] 2. [http://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl99b-recon2.pdf Cortical Surface-Based Analysis II: Inflation, Flattening, and a Surface-Based Coordinate System] 3. [http://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl99-morphing.pdf High-resolution inter-subject averaging and a coordinate system for the cortical surface] 4. [http://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl00-cortical-thickness.pdf Measuring the Thickness of the Human Cerebral Cortex from Magnetic Resonance Images] 5. [http://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] 6. [http://surfer.nmr.mgh.harvard.edu/ftp/articles/montillo02-labeling.pdf Whole Brain Segmentation: Automated Labeling of Neuroanatomical Structures in the Human Brain] 7. [http://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl04-parcellation.pdf Automatically Parcellating the Human Cerebral Cortex] |
* '''''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. * '''''cortical parcellation:''''' * [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl04-parcellation.pdf Automatically Parcellating the Human Cerebral Cortex], Fischl et al., (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 et al., (2006). NeuroImage, in press. * '''''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 et al., (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. * '''''related methodological papers''''' * [http://www.nmr.mgh.harvard.edu/~fischl/reprints/Golland_MICCAI2002.pdf Discriminative Analysis for Image-Based Studies], P. Golland, 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], P. Golland 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], F. Segonne, E. Grimson and B. Fischl, (2003) MICCAI 2003. |
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| 1 Dale, A.M., Fischl, Bruce, Sereno, M.I., (1999). Cortical Surface-Based Analysis I: Segmentation and Surface Reconstruction. NeuroImage 9(2):179-194 | 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 Huntingtons disease], Rosas et al., (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 et al., (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. * [https://surfer.nmr.mgh.harvard.edu/ftp/articles/salat04-thinning.pdf Thinning of the Cerebral Cortex in Aging], Salat et al., (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. |
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| 2 Fischl, Bruce, Sereno, M.I., Dale, A.M., (1999). Cortical Surface-Based Analysis II: Inflation, Flattening, and a Surface-Based Coordinate System. NeuroImage, 9(2):195-207. | |
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| 3 Fischl, Bruce, Sereno, M.I., Tootell, R.B.H., and Dale, A.M., (1999). High-resolution inter-subject averaging and a coordinate system for the cortical surface. Human Brain Mapping, 8:272-284(1990). | |
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| 4 Fischl, Bruce, and Dale, A.M., (2000). Measuring the Thickness of the Human Cerebral Cortex from Magnetic Resonance Images. Proceedings of the National Academy of Sciences, 97:11044-11049. 5 Fischl, Bruce, Liu, Arthur, and Dale, A.M., (2001). Automated Manifold Surgery: Constructing Geometrically Accurate and Topologically Correct Models of the Human Cerebral Cortex. IEEE Transactions on Medical Imaging, 20(1):70-80. 6 Montillo et al., (2002). Whole Brain Segmentation: Automated Labeling of Neuroanatomical Structures in the Human Brain. Neuron, 33:341-355. 7 Fischl et al., (2004). Automatically Parcellating the Human Cerebral Cortex. Cerebral Cortex, 14:11-22. |
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.
cortical parcellation:
[https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl04-parcellation.pdf Automatically Parcellating the Human Cerebral Cortex], Fischl et al., (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 et al., (2006). NeuroImage, in press.
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 et al., (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.
related methodological papers
[http://www.nmr.mgh.harvard.edu/~fischl/reprints/Golland_MICCAI2002.pdf Discriminative Analysis for Image-Based Studies], P. Golland, 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], P. Golland 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], F. Segonne, E. Grimson and B. Fischl, (2003) MICCAI 2003.
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 Huntingtons disease], Rosas et al., (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 et al., (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.
[https://surfer.nmr.mgh.harvard.edu/ftp/articles/salat04-thinning.pdf Thinning of the Cerebral Cortex in Aging], Salat et al., (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.