Tutorials, articles, abstracts¶
Computing¶
Tutorials¶
Matthew Brett. The curious coder's guide to git. 2012–2016. URL: https://matthew-brett.github.io/curious-git.
Matthew Brett. Floating point error. 2012. URL: https://matthew-brett.github.io/teaching/floating_error.html.
Articles¶
Pauli Virtanen, Ralf Gommers, Travis E Oliphant, Matt Haberland, Tyler Reddy, David Cournapeau, Evgeni Burovski, Pearu Peterson, Warren Weckesser, Jonathan Bright, Stéfan J. van der Walt, Matthew Brett, Joshua Wilson, K. Jarrod Millman, Andrew R. J. Nelson Nikolay Mayorov, Eric Jones, Robert Kern, Eric Larson, C J Carey, İlhan Polat, Yu Feng, Eric W. Moore, Jake VanderPlas, Denis Laxalde, Josef Perktold, Robert Cimrman, Ian Henriksen, E. A. Quintero, Charles R. Harris, Anne M. Archibald, Antônio H. Ribeiro, Fabian Pedregosa, Paul van Mulbregt, and SciPy 1.0 Contributors. Scipy 1.0: fundamental algorithms for scientific computing in python. Nature methods, 17(3):261–272, 2020.
Charles R Harris, K Jarrod Millman, Stéfan J van der Walt, Ralf Gommers, Pauli Virtanen, David Cournapeau, Eric Wieser, Julian Taylor, Sebastian Berg, Nathaniel J Smith, Robert Kern, Stephan Hoyer Matti Picus, Marten H. van Kerkwijk, Allan Haldane Matthew Brett, Jaime Fernández del Río, Pearu Peterson Mark Wiebe, Pierre Gérard-Marchant, Tyler Reddy Kevin Sheppard, Warren Weckesser, Hameer Abbasi, Christoph Gohlke, and Travis E. Oliphant. Array programming with numpy. Nature, 585(7825):357–362, 2020.
Eleftherios Garyfallidis, Matthew Brett, Bago Amirbekian, Ariel Rokem, Stéfan van der Walt, Maxime Descoteaux, and Ian Nimmo-Smith. Dipy, a library for the analysis of diffusion mri data. Frontiers in Neuroinformatics, 2014. URL: https://dx.doi.org/10.3389/fninf.2014.00008, doi:10.3389/fninf.2014.00008.
K. Jarrod Millman and Matthew Brett. Analysis of functional magnetic resonance imaging in Python. Computing in Science & Engineering, pages 52–55, 2007. URL: https://dx.doi.org/10.1109/MCSE.2007.63. download publication. download poster.
Abstracts¶
Matthew Brett, Jonathan Taylor, Chris Burns, K. Jarrod Millman, Fernando Perez, Alexis Roche, Bertrand Thirion, and Mark J. D'Esposito. NIPY: an open library and development framework for FMRI data analysis. NeuroImage, 47:S196, 2009. download publication. download poster.
Jonathan E. Taylor, Keith J. Worsley, Matthew Brett, Yann Cointepas, John D. Hunter, K. Jarrod Millman, Jean-Baptiste Poline, and Fernando Perez. BrainPy: an open source environment for the analysis and visualization of human brain data. Neuroimage, 26:763, 2005.
Matthew Brett, Jean-Luc Anton, Romain Valabregue, and Jean-Baptiste Poline. Region of interest analysis using an SPM toolbox. Neuroimage, 16(2):1140–1141, 2002. download publication. download poster.
Functional imaging of movement and thinking¶
Articles¶
Valia Rodriguez Rodriguez, Russell Thompson, Mark Stokes, Matthew Brett, Indira Alvarez, Mitchell Valdes-Sosa, and John Duncan. Absence of face-specific cortical activity in the complete absence of awareness: converging evidence from functional magnetic resonance imaging and event-related potentials. Journal of Cognitive Neuroscience, 24(2):396–415, 2012.
Jessica A Grahn and Matthew Brett. Impairment of beat-based rhythm discrimination in parkinson's disease. Cortex, 45(1):54–61, Jan 2009. URL: https://dx.doi.org/10.1016/j.cortex.2008.01.005, doi:10.1016/j.cortex.2008.01.005.
Rebecca M C Spencer, Timothy Verstynen, Matthew Brett, and Richard Ivry. Cerebellar activation during discrete and not continuous timed movements: an fmri study. Neuroimage, 36(2):378–387, Jun 2007. URL: https://dx.doi.org/10.1016/j.neuroimage.2007.03.009, doi:10.1016/j.neuroimage.2007.03.009.
Jessica A Grahn and Matthew Brett. Rhythm and beat perception in motor areas of the brain. J Cogn Neurosci, 19(5):893–906, May 2007. URL: https://dx.doi.org/10.1162/jocn.2007.19.5.893, doi:10.1162/jocn.2007.19.5.893.
Anja Dove, Matthew Brett, Rhodri Cusack, and Adrian M Owen. Dissociable contributions of the mid-ventrolateral frontal cortex and the medial temporal lobe system to human memory. Neuroimage, 31(4):1790–1801, Jul 2006. URL: https://dx.doi.org/10.1016/j.neuroimage.2006.02.035, doi:10.1016/j.neuroimage.2006.02.035.
Marion L Kellenbach, Matthew Brett, and Karalyn Patterson. Actions speak louder than functions: the importance of manipulability and action in tool representation. J Cogn Neurosci, 15(1):30–46, Jan 2003. URL: https://dx.doi.org/10.1162/089892903321107800, doi:10.1162/089892903321107800. download publication. download poster.
Kim S Graham, Andy C H Lee, Matthew Brett, and Karalyn Patterson. The neural basis of autobiographical and semantic memory: new evidence from three pet studies. Cogn Affect Behav Neurosci, 3(3):234–254, Sep 2003.
Marion L. Kellenbach, Matthew Brett, and Karalyn Patterson. Large, colorful, or noisy? attribute- and modality-specific activations during retrieval of perceptual attribute knowledge. Cogn Affect Behav Neurosci, 1(3):207–221, Sep 2001. download publication. download poster.
Abstracts and conference papers¶
Katja Osswald, John Duncan, Gordon D. Logan, and Matthew Brett. Automatic response selection – functional imaging of practice effects. Abstract Viewer/Itinerary Planner. Washington, DC: Society for Neuroscience. Program No. 163.2. Online, 2002. download publication. download poster.
Anje Dove, James B. Rowe, Matthew Brett, and Adrian M. Owen. Neural correlates of passive and active encoding and retrieval: a 3t fMRI study. NeuroImage, 13(6):S660, 2001.
Matthew Brett, John F. Stein, and David J. Brooks. The role of the lateral premotor cortex in conditional and imitated praxis. NeuroImage, 9:S987, 1998. download publication. download poster.
Matthew Brett, I. Harry Jenkins, John F. Stein, and David J. Brooks. Movement selection without preparation does not activate the sma. NeuroImage, 5:S269, 1997. download publication. download poster.
Methodology¶
Tutorials¶
Matthew Brett. Fourier without the $e^i$. 2016. URL: https://matthew-brett.github.io/teaching/fourier_no_ei.html.
Matthew Brett. Thresholding with the false discovery rate. 2015. URL: https://matthew-brett.github.io/teaching/fdr.html.
Matthew Brett. Notes on the bonferroni threshold. 2015. URL: https://matthew-brett.github.io/teaching/bonferroni_correction.html.
Matthew Brett. Introducing principal components analysis. 2015. URL: https://matthew-brett.github.io/teaching/pca_introduction.html.
Matthew Brett. Convolution. 2015. URL: https://matthew-brett.github.io/teaching/on_convolution.html.
Matthew Brett. Coordinate systems and affines. 2014. URL: https://nipy.org/nibabel/coordinate_systems.html.
Matthew Brett. Thresholding with random field theory. 2013. URL: https://matthew-brett.github.io/teaching/random_fields.html.
Matthew Brett. Notes on "why most published research findings are false". 2013. URL: https://matthew-brett.github.io/teaching/ioannidis_2005.html.
Matthew Brett. Introducing the general linear model. 2013. URL: https://matthew-brett.github.io/teaching/glm_intro.html.
Matthew Brett. What is an r formula? python / r notebook. 2012. URL: https://perrin.dynevor.org/exploring_r_formula.html.
Rhodri Cusack, Matthew Brett, and Katja Osswald. An evaluation of the use of magnetic field maps to undistort echo-planar images. Neuroimage, 18(1):127–142, Jan 2003.
Matthew Brett. Introduction to spm statistics - matlab. 1999–2003. URL: https://imaging.mrc-cbu.cam.ac.uk/imaging/PrinciplesStatistics.
Matthew Brett. Thresholding with random fields - matlab. 1998-2003. URL: https://imaging.mrc-cbu.cam.ac.uk/imaging/PrinciplesRandomFields.
Matthew Brett. Small volume correction using the theory of random fields- matlab. 1998-2003. URL: https://imaging.mrc-cbu.cam.ac.uk/imaging/SmallVolumeCorrection.
Matthew Brett. An introduction to smoothing - matlab. 1998–2003. URL: https://imaging.mrc-cbu.cam.ac.uk/imaging/PrinciplesSmoothing.
Articles and book chapters¶
Jean-Baptiste Poline and Matthew Brett. The general linear model and fmri: does love last forever? NeuroImage, 62(2):871–880, 2012. doi:10.1016/j.neuroimage.2012.01.133. download publication. download poster.
Eleftherios Garyfallidis, Matthew Brett, Marta M. Correia, Guy B. Williams, and Ian Nimmo-Smith. Quickbundles, a method for tractography simplification. Frontiers in Neuroscience, 6:175, 2012.
Christian Schwarzbauer, Toralf Mildner, Wolfgang Heinke, Matthew Brett, and Ralf Deichmann. Dual echo epi–the method of choice for fmri in the presence of magnetic field inhomogeneities? Neuroimage, 49(1):316–326, Jan 2010. URL: https://dx.doi.org/10.1016/j.neuroimage.2009.08.032, doi:10.1016/j.neuroimage.2009.08.032.
Russell A Poldrack, Paul C Fletcher, Richard N Henson, Keith J Worsley, Matthew Brett, and Thomas E Nichols. Guidelines for reporting an fmri study. Neuroimage, 40(2):409–414, Apr 2008. URL: https://dx.doi.org/10.1016/j.neuroimage.2007.11.048, doi:10.1016/j.neuroimage.2007.11.048.
Rebecca M C Spencer, Timothy Verstynen, Matthew Brett, and Richard Ivry. Cerebellar activation during discrete and not continuous timed movements: an fmri study. Neuroimage, 36(2):378–387, Jun 2007. URL: https://dx.doi.org/10.1016/j.neuroimage.2007.03.009, doi:10.1016/j.neuroimage.2007.03.009.
Matthew Brett, William Penny, and Stefan Kiebel. Parametric procedures. In Karl Friston, John Ashburner, Stefan Kiebel, Thomas Nichols, and William Penny, editors, Statistical Parametric Mapping: The Analysis of Functional Brain Images, pages 223 – 231. Elsevier, 2007.
Rebecca Saxe, Matthew Brett, and Nancy Kanwisher. Divide and conquer: a defense of functional localizers. Neuroimage, 30(4):1088–96; discussion 1097–9, May 2006. URL: https://dx.doi.org/10.1016/j.neuroimage.2005.12.062, doi:10.1016/j.neuroimage.2005.12.062.
John A D Aston, Federico E Turkheimer, and Matthew Brett. Hbm functional imaging analysis contest data analysis in wavelet space. Hum Brain Mapp, 27(5):372–379, May 2006. URL: https://dx.doi.org/10.1002/hbm.20244, doi:10.1002/hbm.20244.
Thomas Nichols, Matthew Brett, Jesper Andersson, Tor Wager, and Jean-Baptiste Poline. Valid conjunction inference with the minimum statistic. Neuroimage, 25(3):653–660, Apr 2005. URL: https://dx.doi.org/10.1016/j.neuroimage.2004.12.005, doi:10.1016/j.neuroimage.2004.12.005.
Ferath Kherif, Jean-Baptiste Poline, Sébastien Mériaux, Habib Benali, Guillaume Flandin, and Matthew Brett. Group analysis in functional neuroimaging: selecting subjects using similarity measures. Neuroimage, 20(4):2197–2208, Dec 2003.
Rhodri Cusack, Matthew Brett, and Katja Osswald. An evaluation of the use of magnetic field maps to undistort echo-planar images. Neuroimage, 18(1):127–142, Jan 2003.
Alexander Hammers, Matthias J Koepp, Samantha L Free, Matthew Brett, Mark P Richardson, Claire Labbé, Vincent J Cunningham, David J Brooks, and John Duncan. Implementation and application of a brain template for multiple volumes of interest. Hum Brain Mapp, 15(3):165–174, Mar 2002.
Matthew Brett, Ingrid S Johnsrude, and Adrian M Owen. The problem of functional localization in the human brain. Nat Rev Neurosci, 3(3):243–249, Mar 2002. URL: https://dx.doi.org/10.1038/nrn756, doi:10.1038/nrn756. download publication. download poster.
Federico Turkheimer, Matthew Brett, Dimitris Visvikis, and Vincent J. Cunningham. Statistical estimation of PET images in the wavelet domain. In A. Gjedde, editor, Physiological imaging of the brain with PET, pages 29 – 33. Academic Press, 2001.
Sharon Gustard, M Jalal Fadili, Emma J. Williams, L. D. Hall, T. Adrian Carpenter, Matthew Brett, and Ed T. Bullmore. Effect of slice orientation on reproducibility of fmri motor activation at 3 tesla. Magn Reson Imaging, 19(10):1323–1331, Dec 2001.
Matthew Brett, Alexander P Leff, Chris Rorden, and John Ashburner. Spatial normalization of brain images with focal lesions using cost function masking. Neuroimage, 14(2):486–500, Aug 2001. URL: https://dx.doi.org/10.1006/nimg.2001.0845, doi:10.1006/nimg.2001.0845. download publication. download poster.
Federico E. Turkheimer, Matthew Brett, John A D Aston, Alexander P. Leff, P. A. Sargent, Richard J. Wise, Paul M. Grasby, and Vincent J. Cunningham. Statistical modeling of positron emission tomography images in wavelet space. J Cereb Blood Flow Metab, 20(11):1610–1618, Nov 2000. URL: https://dx.doi.org/10.1097/00004647-200011000-00011, doi:10.1097/00004647-200011000-00011.
Chris Rorden and Matthew Brett. Stereotaxic display of brain lesions. Behav Neurol, 12(4):191–200, 2000. download publication. download poster.
Federico E. Turkheimer, Matthew Brett, D. Visvikis, and Vincent J. Cunningham. Multiresolution analysis of emission tomography images in the wavelet domain. J Cereb Blood Flow Metab, 19(11):1189–1208, Nov 1999. URL: https://dx.doi.org/10.1097/00004647-199911000-00003, doi:10.1097/00004647-199911000-00003.
Abstracts and conference papers¶
Eleftherios Garyfallidis, Matthew Brett, Vassilis Tsiaras, George Vogiatzis, and Ian Nimmo-Smith. Identification of corresponding tracks in diffusion mri tractographies. In Proceedings of the International Society for Magnetic Resonance in Medicine, volume 18. 2010.
Matthew Brett, Ian Nimmo-Smith, Katja Osswald, and Ed T. Bullmore. Model fitting and power in fast event related designs. NeuroImage, 19(2):abstract 791, 2003. download publication. download poster.
M. Jalal Fadili, Ed T. Bullmore, and Matthew Brett. Wavelet methods for characterising mono-and poly-fractal noise structures in shortish time series: an application to functional MRI. In Image Processing, 2001. Proceedings. 2001 International Conference on, pages 225–228. 2002.
Ingrid S. Johnsrude, Rhodri Cusack, P. Morosan, Debbie Hall, Matthew Brett, Karl Zilles, and Richard S. J. Frackowiak. Cytoarchitectonic region-of-interest analysis of auditory imaging data. NeuroImage, 13(6):S897, 2001.
Matthew Brett, Kalina Christoff, Rhodri Cusack, and Jack Lancaster. Using the Talairach atlas with the MNI template. Neuroimage, 13(6):S85, 2001. download publication. download poster.
Matthew Brett, Peter Bloomfield, David J. Brooks, John F. Stein, and Paul Grasby. Scan order effects in PET activation studies are caused by motion artifact. NeuroImage, 9:S56, 1999. download publication. download poster.
About other things¶
Matthew Brett and Sallie Baxendale. Motherhood and memory: a review. Psychoneuroendocrinology, 26(4):339–362, May 2001. download publication. download poster.
M. Brett, M. R. Persey, M. M. Reilly, T. Revesz, D. R. Booth, S. E. Booth, P. N. Hawkins, M. B. Pepys, and J. A. Morgan-Hughes. Transthyretin leu12pro is associated with systemic, neuropathic and leptomeningeal amyloidosis. Brain, 122 ( Pt 2):183–190, Feb 1999. download publication. download poster.
M. Brett, R. Greenwood, J. Powell, and P. Morris. Late functional recovery with a novel community rehabilitation programme after herpes simplex encephalitis. Clinical Rehabilitation, 9(3):267–270, Aug 1995. doi:10.1177/026921559500900315.
Alistair Chesser and Matthew Brett. Clinical teaching in context: a factor analysis of student ratings. Research in Medical Education Conference (RIME). In Proceedings of the twenty-eighth annual conference. Washington: Association of American Medical Colleges. 1989.