MRI reading list

You can find another version of this list as a collection on ScienceOpen.

Experimental design and analytic flexibility

Carp J (2012) On the plurality of (methodological) worlds: Estimating the analytic flexibility of fMRI experiments. Frontiers in Neuroscience 6:1-13. https://doi.org/10.3389/fnins.2012.00149

Simmons JP, Nelson LD, Simonsohn U (2011) False-positive psychology: Undisclosed flexibility in data collection and analysis allows presenting anything as significant. Psychological Science 22:1359-1366. https://doi.org/10.1177/0956797611417632

Power

Liu TT, Frank LR (2004) Efficiency, power, and entropy in event-related FMRI with multiple trial types: Part I: theory. NeuroImage 21:387-400. http://doi.org/10.1016/j.neuroimage.2003.09.030

Liu TT (2004) Efficiency, power, and entropy in event-related fMRI with multiple trial types Part II: Design of experiments. NeuroImage 21:401–413. http://dx.doi.org/10.1016/j.neuroimage.2003.09.031

Spatial normalization

Ashburner J (2007) A fast diffeomorphic image registration algorithm. NeuroImage 38:95-113. http://doi.org/10.1016/j.neuroimage.2007.07.007

Crinion J, Ashburner J, Leff A, Brett M, Price C, Friston K (2007) Spatial normalization of lesioned brains: Performance evaluation and impact on fMRI analyses. NeuroImage 37:866-875. http://doi.org/10.1016/j.neuroimage.2007.04.065

Klein A, Andersson J, Ardekani BA, Ashburner J, Avants B, Chiang M-C, Christensen GE, Collins DL, Gee J, Hellier P, Song JH, Jenkinson M, Lepage C, Rueckert D, Thompson P, Vercauteren T, Woods RP, Mann JJ, Parsey RV (2009) Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration. NeuroImage 46:786-802. http://dx.doi.org/10.1016/j.neuroimage.2008.12.037

Tissue-class segmentation

Ashburner J, Friston KJ (2005) Unified segmentation. NeuroImage 26:839-851. http://doi.org/10.1016/j.neuroimage.2005.02.018

Ashburner J, Friston KJ (2009) Computing average shaped tissue probability templates. NeuroImage 45:333-341.

Motion

Alexander-Bloch A, Clasen L, Stockman M, Ronan L, Lalonde F, Giedd J, Raznahan A (2016) Subtle in-scanner motion biases automated measurement of brain anatomy from in vivo MRI. Human Brain Mapping 37:2385-2397. http://onlinelibrary.wiley.com/enhanced/doi/10.1002/hbm.23180

Power JD, Barnes KA, Snyder AZ, Schlaggar BL, Petersen SE (2012) Spurious but systematic correlations in functional connectivity MRI networks arise from subject motion. NeuroImage 59:2142-2154. http://dx.doi.org/10.1016/j.neuroimage.2011.10.018

Siegel JS, Power JD, Dubis JW, Vogel AC, Church JA, Schlaggar BL, Petersen SE (2014) Statistical improvements in functional magnetic resonance imaging analyses produced by censoring high-motion data points. Hum Brain Mapp 35:1981-1996. http://dx.doi.org/10.1002/hbm.22307

Slice-timing correction

Sladky R, Friston KJ, Tröstl J, Cunnington R, Moser E, Windischberger C (2011) Slice-timing effects and their correction in functional MRI. NeuroImage 58:588-594. http://dx.doi.org/10.1016/j.neuroimage.2011.06.078

Correction for multiple comparisons

Bennett CM, Wolford GL, Miller MB (2009) The principled control of false positives in neuroimaging. Social Cognitive and Affective Neuroscience 4:417-422. http://dx.doi.org/10.1093/scan/nsp053

Bennett CM, Baird AA, Miller MB, Wolford GL (2009) Neural correlates of interspecies perspective taking in the post-mortem Atlantic Salmon: An argument for multiple comparisons correction. Journal of Serendipitous and Unexpected Results 1:1-5. http://jpeelle.net/reprints/Bennett-2011-Neural_correlates_of_interspecies_perspective_taking.pdf

Chumbley JR, Friston KJ (2009) False discovery rate revisited: FDR and topological inference using Gaussian random fields. NeuroImage 44:62-70. http://dx.doi.org/10.1016/j.neuroimage.2008.05.021

Nichols T, Hayasaka S (2003) Controlling the familywise error rate in functional neuroimaging: a comparative review. Statistical methods in medical research 12:419-446. http://dx.doi.org/10.1191/0962280203sm341ra

Nichols TE, Holmes AP (2002) Nonparametric permutation tests for functional neuroimaging: A primer with examples. Hum Brain Mapp 15:1-25. http://dx.doi.org/10.1002/hbm.1058

Worsley KJ (1996) The geometry of random images. Chance 9:27-39. http://dx.doi.org/10.1080/09332480.1996.10542483

Anatomical localization

Brett M, Johnsrude IS, Owen AM (2002) The problem of functional localization in the human brain. Nature Reviews Neuroscience 3:243-249. http://dx.doi.org/10.1038/nrn756

Devlin JT, Poldrack RA (2007) In praise of tedious anatomy. NeuroImage 37:1033-1041. http://dx.doi.org/10.1016/j.neuroimage.2006.09.055

Data reporting, sharing, etc.

Gorgolewski KJ, Varoquaux G, Rivera G, Schwarz Y, Ghosh SS, Maumet C, Sochat VV, Nichols TE, Poldrack RA, Poline J-B, Yarkoni T, Margulies DS (2015) NeuroVault.org: a web-based repository for collecting and sharing unthresholded statistical maps of the human brain. Front Neuroinform 9:8. http://dx.doi.org/10.3389/fninf.2015.00008

Pernet CR, Poline J-B (2015) Improving functional magnetic resonance imaging reproducibility. GigaScience 4:15. http://dx.doi.org/10.1186/s13742-015-0055-8

Poldrack RA, Fletcher PC, Henson RN, Worsley KJ, Brett M, Nichols TE (2008) Guidelines for reporting an fMRI study. NeuroImage 40:409-414. http://dx.doi.org/10.1016/j.neuroimage.2007.11.048

Auditory fMRI

Peelle JE (2014) Methodological challenges and solutions in auditory functional magnetic resonance imaging. Frontiers in Neuroscience 8:253. http://dx.doi.org/10.3389/fnins.2014.00253

Voxel-based morphometry

Mechelli A, Price CJ, Friston KJ, Ashburner J (2005) Voxel-based morphometry of the human brain: Methods and applications. Current Medical Imaging Reviews 1:105-113. http://dx.doi.org/10.2174/1573405054038726

Ridgway GR, Henley SMD, Rohrer JD, Scahill RI, Warren JD, Fox NC (2008) Ten simple rules for reporting voxel-based morphometry studies. NeuroImage 40, 1429–1435. http://dx.doi.org/10.1016/j.neuroimage.2008.01.003

Other structural imaging techniques

Weiskopf N, Mohammadi S, Lutti A, Callaghan MF (2015) Advances in MRI-based computational neuroanatomy: from morphometry to in-vivo histology. Current Opinion in Neurology 28:313-322. http://dx.doi.org/10.1097/WCO.0000000000000222

Other statistical papers and pitfalls

Henson RNA, Penny W. ANOVAs in SPM. Technical report. PDF

Kriegeskorte N, Simmons WK, Bellgowan PSF, Baker CI (2009) Circular analysis in systems neuroscience: The dangers of double dipping. Nat Neurosci 12:535-540. (along with supplemental material) http://dx.doi.org/10.1038/nn.2303

Pernet CR (2014) Misconceptions in the use of the General Linear Model applied to functional MRI: a tutorial for junior neuro-imagers. Front Neurosci 8:1. http://dx.doi.org/10.3389/fnins.2014.00001