The DOI matches its Crossref record; 18 of the 18 references it cites were found in a registry or an index.
FSL
Open accessAbstract
FSL (the FMRIB Software Library) is a comprehensive library of analysis tools for functional, structural and diffusion MRI brain imaging data, written mainly by members of the Analysis Group, FMRIB, Oxford. For this NeuroImage special issue on "20 years of fMRI" we have been asked to write about the history, developments and current status of FSL. We also include some descriptions of parts of FSL that are not well covered in the existing literature. We hope that some of this content might be of interest to users of FSL, and also maybe to new research groups considering creating, releasing and supporting new software packages for brain image analysis.
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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 [72]
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“While there are many sophisticated tools to compute these registrations such as FSL (Jenkinson et al., 2012) and ANTs (Avants et al., 2009), the performance is limited by nontrivial factors.”
From Quantitative mapping of the brain’s structural connectivity using diffusion MRI tractography: A review (2022) · cites this paper as Jenkinson et al., 2012
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Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
Benjamini, Y., & Hochberg, Y. (1995) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.2517-6161.1995.tb02031.x · Cited by 109,482
Advances in functional and structural MR image analysis and implementation as FSL
Smith, S. M., Jenkinson, M., Woolrich, M. W., Beckmann, C. F., Behrens, T. E. J., Johansen-Berg, H., Bannister, P. R., De Luca, M., Drobnjak, I., Flitney, D. E., et al. (2004) · NeuroImage · doi:10.1016/j.neuroimage.2004.07.051 · Cited by 13,630
Self-citationVoxel-Based Morphometry—The Methods
Ashburner, J., & Friston, K. J. (2000) · NeuroImage · doi:10.1006/nimg.2000.0582 · Cited by 8,676
Nonparametric permutation tests for functional neuroimaging: A primer with examples
Nichols, T. E., & Holmes, A. P. (2002) · Human Brain Mapping · doi:10.1002/hbm.1058 · Cited by 6,256
Nonrigid registration using free-form deformations: application to breast mr images
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SMITH, S., & NICHOLS, T. (2009) · NeuroImage · doi:10.1016/j.neuroimage.2008.03.061 · Cited by 5,250
Self-citationA Voxel-Based Morphometric Study of Ageing in 465 Normal Adult Human Brains
Good, C. D., Johnsrude, I. S., Ashburner, J., Henson, R. N. A., Friston, K. J., & Frackowiak, R. S. J. (2001) · NeuroImage · doi:10.1006/nimg.2001.0786 · Cited by 4,561
Bayesian analysis of neuroimaging data in FSL
Woolrich, M. W., Jbabdi, S., Patenaude, B., Chappell, M., Makni, S., Behrens, T., Beckmann, C., Jenkinson, M., & Smith, S. M. (2009) · NeuroImage · doi:10.1016/j.neuroimage.2008.10.055 · Cited by 2,385
Self-citationA three-dimensional statistical analysis for CBF activation studies in human brain
Worsley, K. J., Evans, A. C., Marrett, S., & Neelin, P. (1992) · Journal of Cerebral Blood Flow & Metabolism · doi:10.1038/jcbfm.1992.127 · Cited by 2,036
Assessing the significance of focal activations using their spatial extent
Friston, K. J., Worsley, K. J., Frackowiak, R. S. J., Mazziotta, J. C., & Evans, A. C. (1994) · Human Brain Mapping · doi:10.1002/hbm.460010306 · Cited by 1,907
Correction for geometric distortion in echo planar images from B0 field variations
Jezzard, P., & Balaban, R. S. (1995) · Magnetic Resonance in Medicine · doi:10.1002/mrm.1910340111 · Cited by 1,428
Anatomically related grey and white matter abnormalities in adolescent-onset schizophrenia
Douaud, G., Smith, S. M., Jenkinson, M., Behrens, T. E. J., Johansen‐Berg, H., Vickers, J., James, S., Voets, N., Watkins, K. E., Matthews, P. M., et al. (2007) · Brain · doi:10.1093/brain/awm184 · Cited by 781
Self-citationLinked independent component analysis for multimodal data fusion
Groves, A. R., Beckmann, C. F., Smith, S. M., & Woolrich, M. W. (2011) · NeuroImage · doi:10.1016/j.neuroimage.2010.09.073 · Cited by 319
Self-citationAn Evaluation of the Use of Magnetic Field Maps to Undistort Echo-Planar Images
Cusack, R., Brett, M., & Osswald, K. (2002) · NeuroImage · doi:10.1006/nimg.2002.1281 · Cited by 219
Woolrich, M. W., Behrens, T. E. J., Beckmann, C. F., & Smith, S. M. (2005) · IEEE Transactions on Medical Imaging · doi:10.1109/tmi.2004.836545 · Cited by 168
Self-citationAdjusting the effect of nonstationarity in cluster-based and TFCE inference
Salimi‐Khorshidi, G., Smith, S. M., & Nichols, T. E. (2010) · NeuroImage · doi:10.1016/j.neuroimage.2010.09.088 · Cited by 150
Self-citationEvidence for abnormalities of cortical development in adolescent-onset schizophrenia
Voets, N., Hough, M., Douaud, G., Matthews, P. M., James, A. C., Winmill, L., Webster, P., & Smith, S. M. (2008) · NeuroImage · doi:10.1016/j.neuroimage.2008.08.013 · Cited by 145
Self-citationYang, D., Meng, G., Zhang, S., et al. (2007) · Chemical Communications · doi:10.1039/b614147a · Cited by 47
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The minimal preprocessing pipelines for the Human Connectome Project
Glasser, M. F., Sotiropoulos, S. N., Wilson, J. A., Coalson, T. S., Fischl, B., Andersson, J. L., Xu, J., Jbabdi, S., Webster, M., Polimeni, J. R., et al. (2013) · NeuroImage · doi:10.1016/j.neuroimage.2013.04.127 · Cited by 5,253
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Esteban, O., Markiewicz, C. J., Blair, R. W., Moodie, C. A., Isik, A. I., Erramuzpe, A., Kent, J. D., Goncalves, M., DuPre, E., Snyder, M., et al. (2019) · Nature Methods · doi:10.1038/s41592-018-0235-4 · Cited by 3,905
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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
Metadata
- Authors
- Jenkinson, M., Beckmann, C. F., Behrens, T. E. J., Woolrich, M. W., & Smith, S. M.
- Affiliations
- University of Oxford (GB)
- Corresponding author
- Jenkinson, Mark
- Venue
- NeuroImage
- Publisher
- Elsevier BV
- Published
- 2012-08
- Volume
- 62
- Issue
- 2
- Pages
- 782-790
- ISSN
- 1053-8119 (ISSN-L)
- OpenAlex
- W2977883299
- Cited by
- 11,314
- References
- 18
- Citations by year
- 2026: 995 · 2025: 1331 · 2024: 1189 · 2023: 1077 · 2022: 1062 · 2021: 1090 · 2020: 1024 · 2019: 827 · 2018: 713 · 2017: 592 · 2016: 531 · 2015: 456 · 2014: 269 · 2013: 142 · 2012: 10
- FWCI
- 102.30
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- NeuroImage (publishedVersion)
- PubMed (publishedVersion)
- HAL (submittedVersion, other-oa)
- Funders
- Engineering and Physical Sciences Research Council (EP/F05727X/1)
- Topics
- Health Sciences › Medicine › Radiology, Nuclear Medicine and Imaging › Advanced MRI Techniques and Applications
- Health Sciences › Medicine › Radiology, Nuclear Medicine and Imaging › Advanced Neuroimaging Techniques and Applications
- Life Sciences › Neuroscience › Cognitive Neuroscience › Functional Brain Connectivity Studies
- Keywords
- FSL, functional MRI, structural MRI, diffusion MRI, software development history, open source software
- MeSH terms
- Brain, Brain Mapping, Humans, Image Processing, Computer-Assisted, Software, Diffusion Magnetic Resonance Imaging, History, 20th Century, History, 21st Century
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