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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]
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“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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Cites
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Brain insulin responsiveness is linked to age and peripheral insulin sensitivity
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Visual temporal frequency preference shows a distinct cortical architecture using fMRI
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Laminar specificity of the auditory perceptual awareness negativity: a biophysical modeling study
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“The manifold of cerebral cortical surface data was first derived through brain tissue segmentation (gray matter, white matter, and cerebral spinal fluid – CSF), followed by cortical surface reconstruction using FreeSurfer 5.3 (Fischl, 2012).”
MethodInfluentialJoint image synthesis and fusion with converted features for Alzheimer’s disease diagnosis
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Establishing the relationship between brain cellular senescence and brain structure
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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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
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