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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. * [https://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. * [https://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. * [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://archpsyc.ama-assn.org/cgi/content/abstract/60/9/878 Regionally Localized Thinning of the Cerebral Cortex in Schizophrenia], Kuperberg et al., (2003). Archives of General Psychiatry, 60:878-888. * [http://neurology.org/cgi/content/abstract/58/5/695 Regional and progressive thinning of the cortical ribbon in Huntingtons disease], Rosas et al., (2002). Neurology, 58:695-701. |
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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 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. 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). 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. |
* '''''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. * [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl04-segmentation.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 Jul;22(3):1060-75. |
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.
[https://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.
[https://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.
[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://archpsyc.ama-assn.org/cgi/content/abstract/60/9/878 Regionally Localized Thinning of the Cerebral Cortex in Schizophrenia], Kuperberg et al., (2003). Archives of General Psychiatry, 60:878-888.
[http://neurology.org/cgi/content/abstract/58/5/695 Regional and progressive thinning of the cortical ribbon in Huntingtons disease], Rosas et al., (2002). Neurology, 58:695-701.
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.
[https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl04-segmentation.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 Jul;22(3):1060-75.