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FreeSurfer
Open accessAbstract
FreeSurfer is a suite of tools for the analysis of neuroimaging data that provides an array of algorithms to quantify the functional, connectional and structural properties of the human brain. It has evolved from a package primarily aimed at generating surface representations of the cerebral cortex into one that automatically creates models of most macroscopically visible structures in the human brain given any reasonable T1-weighted input image. It is freely available, runs on a wide variety of hardware and software platforms, and is open source.
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“The most popularly used cortical parcellation is the Freesurfer Desikan-Killiany cortical parcellation (Desikan et al., 2006; Fischl, 2012), while many other cortical parcellation schemes have also been widely used (Destrieux et al., 2010; Shattuck et al., 2008; Tzourio-Mazoyer et al., 2002).”
From Quantitative mapping of the brain’s structural connectivity using diffusion MRI tractography: A review (2022) · cites this paper as Fischl, 2012
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“All data sets were corrected for head motion, eddy currents and susceptibility distortions and are, in general, of very high quality69–73.”
From Tractography-based connectomes are dominated by false-positive connections (2016) · cites this paper as [71]
Experimental — accuracy not yet measuredIn the citing paper
“Surface based registrations that take into account the sulcal and gyral anatomy also help mitigate these confounds, and may be the future direction of the field (Fischl, 2012; Van Essen, 2012).”
From Development of large-scale functional networks from birth to adulthood: A guide to the neuroimaging literature (2017) · cites this paper as Fischl, 2012
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Self-citationCortical Surface Shape Analysis Based on Spherical Wavelets
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Self-citationLocalization of focal epileptic discharges using functional connectivity magnetic resonance imaging
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Selective Disruption of the Cerebral Neocortex in Alzheimer's Disease
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Self-citationA method for identifying geometrically simple surfaces from three-dimensional images
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Regional cortical thickness matters in recall after months more than minutes
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Self-citationImproved tractography alignment using combined volumetric and surface registration
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Self-citationSize does matter in the long run
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Self-citationTopological Correction of Subcortical Segmentation
Ségonne, F., Grimson, E., & Fischl, B. R. (2003) · Lecture notes in computer science · doi:10.1007/978-3-540-39903-2_85 · Cited by 33
Self-citationNeuroanatomical aging: Universal but not uniform
Walhovd, K. B., Fjell, A. M., Reinvang, I., Lundervold, A., Dale, A. M., Quinn, B. T., Salat, D. H., Makris, N., & Fischl, B. R. (2005) · Neurobiology of Aging · doi:10.1016/j.neurobiolaging.2005.05.018 · Cited by 26
Self-citationActive Contours Under Topology Control Genus Preserving Level Sets
Ségonne, F., Pons, J.-P., Grimson, E., et al. (2005) · Lecture notes in computer science · doi:10.1007/11569541_15 · Cited by 17
Cortical Thickness Reduction of Normal Appearing Cortex in Patients with Polymicrogyria
Oliveira, P. P. D. M., Valente, K. D. R., Shergill, S. S., Leite, C. D. C., & Amaro, E. (2009) · Journal of Neuroimaging · doi:10.1111/j.1552-6569.2009.00372.x · Cited by 12
Task-Optimal Registration Cost Functions
Yeo, B. T. T., Sabuncu, M. R., Golland, P., & Fischl, B. R. (2009) · Lecture notes in computer science · doi:10.1007/978-3-642-04268-3_74 · Cited by 6
Self-citationKremen, W. S., Prom‐Wormley, E. C., Panizzon, M. S., et al. (2009) · NeuroImage · doi:10.1016/j.neuroimage.2009.12.015 · Cited by 3
High-resolution intersubject averaging and a coordinate system for the cortical surface
Fischl, B., Sereno, M. I., Tootell, R. B. H., & Dale, A. M. (1999) · Human Brain Mapping · doi:10.1002/(sici)1097-0193(1999)8:4
Self-citation
Flagged first, then by citations
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- Postelnicu, 2009, Combined volumetric and surface registration, IEEE Trans. Med. Imaging, 28, 508, 10.1109/TMI.2008.2004426 · DOI
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A multi-modal parcellation of human cerebral cortex
Glasser, M. F., Coalson, T. S., Robinson, E. C., Hacker, C. D., Harwell, J., Yacoub, E., Ugurbil, K., Andersson, J., Beckmann, C. F., Jenkinson, M., et al. (2016) · Nature · doi:10.1038/nature18933 · Cited by 5,111
Local-global parcellation of the human cerebral cortex from intrinsic functional connectivity MRI
Schaefer, A., Kong, R., Gordon, E. M., Laumann, T. O., Zuo, X.-N., Holmes, A. J., Eickhoff, S. B., & Yeo, B. T. T. (2018) · Cerebral Cortex · doi:10.1093/cercor/bhx179 · Cited by 3,657
fMRIPrep: A robust preprocessing pipeline for functional MRI
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MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation
Tournier, J.-D., Smith, R., Raffelt, D., Tabbara, R., Dhollander, T., Pietsch, M., Christiaens, D., Jeurissen, B., Yeh, C.-H., & Connelly, A. (2019) · NeuroImage · doi:10.1016/j.neuroimage.2019.116137 · Cited by 2,974
Situating the default-mode network along a principal gradient of macroscale cortical organization
Margulies, D. S., Ghosh, S. S., Goulas, A., Falkiewicz, M., Huntenburg, J. M., Langs, G., Bezgin, G., Eickhoff, S. B., Castellanos, F. X., Petrides, M., et al. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1608282113 · Cited by 2,321
Metadata
- Authors
- Fischl, B.
- Affiliations
- Harvard University (US)
- Corresponding author
- Fischl, Bruce
- ORCID
- Fischl, Bruce
- Venue
- NeuroImage
- Publisher
- Elsevier BV
- Published
- 2012-08
- Volume
- 62
- Issue
- 2
- Pages
- 774-781
- ISSN
- 1053-8119 (ISSN-L)
- PMC
- PMC3685476
- OpenAlex
- W4241074797
- Semantic Scholar
- 771b3c73fbaba12f5d65db39401ee9cddb224554
- Cited by
- 9,526
- References
- 96
- Citations by year
- 2026: 1247 · 2025: 1431 · 2024: 1203 · 2023: 1051 · 2022: 998 · 2021: 912 · 2020: 688 · 2019: 512 · 2018: 491 · 2017: 332 · 2016: 255 · 2015: 188 · 2014: 131 · 2013: 66 · 2012: 9
- FWCI
- 17.92
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- NeuroImage (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Center for Research Resources (P41-RR14075, BIRN002, U24 RR021382)
- National Institute on Aging (AG022381)
- National Institute of Neurological Disorders and Stroke (1S10RR023401, R01 NS052585-01, 1R01NS070963, 1S10RR023043, 1S10RR019307, 1R21NS072652-01)
- Ellison Medical Foundation
- National Institute of Biomedical Imaging and Bioengineering (R01EB006758)
- Topics
- Physical Sciences › Computer Science › Computer Vision and Pattern Recognition › Medical Image Segmentation Techniques
- Health Sciences › Medicine › Radiology, Nuclear Medicine and Imaging › Advanced Neuroimaging Techniques and Applications
- Life Sciences › Neuroscience › Cognitive Neuroscience › Functional Brain Connectivity Studies
- Keywords
- FreeSurfer, neuroimaging data analysis, cortical surface reconstruction, T1-weighted imaging, brain connectivity, open source software
- MeSH terms
- Algorithms, Brain, Brain Mapping, Humans, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Software, History, 20th Century, History, 21st Century
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