From FMRI Methods

Here is a short list of refereces which may be useful to consult with respect to different aspects of fMRI use. This list is not nor it will ever be exhaustive. Only some exemplar references are suggested and the reader is strongly encouraged to search for additional literature.

Contents 1 BOOKS 2 ARTICLES 2.1 Why, when and how to use fMRI 2.2 Basics on conducting an fMRI study 2.3 More specific fMRI methods 2.3.1 The quest for independence 2.3.2 Region-of-interest analysis and the use of functional localizers 2.3.3 Conjunction analysis 2.3.4 Bayesian analysis 2.3.5 Information-based and multivoxel pattern analysis 2.3.6 Connectivity 2.4 Reporting an fMRI study 2.4.1 Anatomy matters 2.5 Interpreting results from an fMRI study 2.6 Combining fMRI with other methods

BOOKS

Buxton, RB (2002) An Introduction to Functional Magnetic Resonance Imaging: Principles and Techniques. Cambridge University Press.

Faro SH, Mohamed, FB (2005). Functional MRI: Basic Principles and Clinical Applications. Springer-Verlag.

Friston KJ (2006) Statistical Parametric Mapping: The Analysis of Functional Brain Images. Academic Press.

Huettel SA, Song AW, McCarthy, G (2004) Functional Magnetic Resonance Imaging. Sinauer Associates.

Jezzard P, Matthews, PM, Smith, SM (2003) Functional MRI: An Introduction to Methods. Oxford University Press:

Moonen CTW, Bandettini PA (2000) Functional MRI. Springer.

ARTICLES

Why, when and how to use fMRI

Bandettini, PA (in press) What's new in neuroimaging methods? Annals of the NY Academy of Sciences: The Year in Cognitive Neuroscience 2009.

Friston K (2002) Beyond phrenology: What can neuroimaging tell us about distributed circuitry? Annual Review of Neuroscience 25:221-250.

Henson R (2005) What can functional neuroimaging tell the experimental psychologist? Q J Exp Psychol A 58:193-233.

Henson R (2006) Forward inference using functional neuroimaging: dissociations versus associations. Trends Cogn Sci 10:64-69.

Horwitz B, Friston KJ, Taylor JG (2000) Neural modeling and functional brain imaging: an overview. Neural Netw 13:829-846.

Logothetis NK (2008) What we can do and what we cannot do with fMRI. Nature 453:869-878.

Menon RS (2001) Imaging function in the working brain with fMRI. Curr Opin Neurobiol 11:630-636.

Poldrack RA (2006) Can cognitive processes be inferred from neuroimaging data? Trends Cogn Sci 10:59-63.

Poldrack RA (2008) The role of fMRI in cognitive neuroscience: where do we stand? Curr Opin Neurobiol 18:223-227.

Basics on conducting an fMRI study

Amaro E, Barker GJ (2006) Study design in MRI: Basic principles. Brain and Cognition 60:220-232.

Dale AM (1999) Optimal experimental design for event-related fMRI. Human Brain Mapping 8:109-114.

Friston KJ (2005) Models of brain function in neuroimaging. Annual Review of Psychology 56:57-87.

Ramsey NF, Hoogduin H, Jansma JM (2002) Functional MRI experiments: acquisition, analysis and interpretation of data. Eur Neuropsychopharmacol 12:517-526.

More specific fMRI methods

Aguirre GK, Zarahn E, D'Esposito M (1998) The variability of human, BOLD hemodynamic responses. Neuroimage 8:360-369.

Bandettini PA, Birn RM, Kelley D, Saad ZS (2002) Dynamic nonlinearities in BOLD contrast: neuronal or hemodynamic? Brain Activation and Cbf Control, Proceedings 1235:73-85.

Birn RM, Cox RW, Bandettini PA (2002) Detection versus estimation in event-related fMRI: choosing the optimal stimulus timing. Neuroimage 15:252-264.

Bosch V (2000) Statistical analysis of multi-subject fMRI data: assessment of focal activations. J Magn Reson Imaging 11:61-64.

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

Cox RW, Jesmanowicz A, Hyde JS (1995) Real-time functional magnetic resonance imaging. Magn Reson Med 33:230-236.

deCharms RC (2008) Applications of real-time fMRI. Nat Rev Neurosci 9:720-729.

Donaldson DI (2004) Parsing brain activity with fMRI and mixed designs: what kind of a state is neuroimaging in? Trends Neurosci 27:442-444.

Eickhoff SB, Paus T, Caspers S, Grosbras MH, Evans AC, Zilles K, Amunts K (2007) Assignment of functional activations to probabilistic cytoarchitectonic areas revisited. Neuroimage 36:511-521.

Friston KJ, Fletcher P, Josephs O, Holmes A, Rugg MD, Turner R (1998) Event-related fMRI: characterizing differential responses. Neuroimage 7:30-40.

Friston KJ, Holmes AP, Poline JB, Grasby PJ, Williams SC, Frackowiak RS, Turner R (1995) Analysis of fMRI time-series revisited. Neuroimage 2:45-53.

Friston KJ, Price CJ, Fletcher P, Moore C, Frackowiak RSJ, Dolan RJ (1996) The trouble with cognitive subtraction. Neuroimage 4:97-104.

Friston KJ, Stephan KE, Lund TE, Morcom A, Kiebel S (2005) Mixed-effects and fMRI studies. Neuroimage 24:244-252.

Glover GH (1999) Deconvolution of impulse response in event-related BOLD fMRI. Neuroimage 9:416-429.

Hasson U, Nir Y, Levy I, Fuhrmann G, Malach R (2004) Intersubject synchronization of cortical activity during natural vision. Science 303:1634-1640.

Henson R, Rugg MD, Friston KJ (2001) The choice of basis functions in event-related fMRI. Neuroimage 13:S149-S149.

Josephs O, Henson RN (1999) Event-related functional magnetic resonance imaging: modelling, inference and optimization. Philos Trans R Soc Lond B Biol Sci 354:1215-1228.

Josephs O, Turner R, Friston K (1997) Event-related fMRI. Human Brain Mapping 5:243-248.

Laurienti PJ, Burdette JH, Maldjian JA (2003) Separating neural processes using mixed event-related and epoch-based fMRI paradigms. J Neurosci Methods 131:41-50.

Mechelli A, Henson RN, Price CJ, Friston KJ (2003a) Comparing event-related and epoch analysis in blocked design fMRI. Neuroimage 18:806-810.

Mechelli A, Price CJ, Henson RN, Friston KJ (2003b) Estimating efficiency a priori: a comparison of blocked and randomized designs. Neuroimage 18:798-805.

Neumann J, Lohmann G, Zysset S, von Cramon DY (2003) Within-subject variability of BOLD response dynamics. Neuroimage 19:784-796.

Nichols T, Hayasaka S (2003) Controlling the familywise error rate in functional neuroimaging: a comparative review. Statistical Methods in Medical Research 12:419-446.

Pollmann S, Dove A, von Cramon DY, Wiggins CJ (2000) Event-related fMRI: Comparison of conditions with varying BOLD overlap. Human Brain Mapping 9:26-37.

Pollmann S, Wiggins CJ, Norris DG, von Cramon DY, Schubert T (1998) Use of short intertrial intervals in single-trial experiments: A 3T fMRI-study. Neuroimage 8:327-339.

Rosen BR, Buckner RL, Dale AM (1998) Event-related functional MRI: past, present, and future. Proceedings of the National Academy of Sciences of the United States of America 95:773-780.

Ugurbil K, Garwood M, Ellermann J, Hendrich K, Hinke R, Hu XP, Kim SG, Menon R, Merkle H, Ogawa S, Salmi R (1993) Imaging at High Magnetic-Fields - Initial Experiences at 4-T. Magnetic Resonance Quarterly 9:259-277.

Visscher KM, Miezin FM, Kelly JE, Buckner RL, Donaldson DI, McAvoy MP, Bhalodia VM, Petersen SE (2003) Mixed blocked/event-related designs separate transient and sustained activity in fMRI. Neuroimage 19:1694-1708.

Wager TD, Lindquist M, Kaplan L (2007) Meta-analysis of functional neuroimaging data: current and future directions. Social Cognitive and Affective Neuroscience 2:150-158.

Wager TD, Nichols TE (2003) Optimization of experimental design in fMRI: a general framework using a genetic algorithm. Neuroimage 18:293-309.

Weiskopf N, Veit R, Erb M, Mathiak K, Grodd W, Goebel R, Birbaumer N (2003) Physiological self-regulation of regional brain activity using real-time functional magnetic resonance imaging (fMRI): methodology and exemplary data. Neuroimage 19:577-586.

Worsley KJ, Friston KJ (1995) Analysis of fMRI time-series revisited--again. Neuroimage 2:173-181.

Worsley KJ, Liao CH, Aston J, Petre V, Duncan GH, Morales F, Evans AC (2002) A general statistical analysis for fMRI data. Neuroimage 15:1-15.

Zarahn E, Aguirre G, D'Esposito M (1997a) A trial-based experimental design for fMRI. Neuroimage 6:122-138.

Zarahn E, Aguirre GK, D'Esposito M (1997b) Empirical analyses of BOLD fMRI statistics. I. Spatially unsmoothed data collected under null-hypothesis conditions. Neuroimage 5:179-197.

The quest for independence

Kriegeskorte N, Simmons WK, Bellgowan PSF, Baker CI (2009) Circular analysis in systems neuroscience: the dangers of double dipping. Nature Neuroscience 12:535-540.

Vul E, Harris C, Winkielman P, Pashler, H (2009) Puzzlingly high correlations in fMRI studies of emotion, personality, and social cognition (The paper formerly known as "Voodoo correlations in social neuroscience"). Perspectives on Psychological Science 4,3:274-290.

Commentaries on Vul et al (2009):

Barret LF (2009) Understanding the Mind by Measuring the Brain: Lessons From Measuring Behavior (Commentary on Vul et al. 2009). Perspectives on Psychological Science 4,3:314-318.

Jabbi M, Keysers C, Singer T, Stephan KE (in prep.) Response to “Voodoo Correlations in Social Neuroscience” by Vul et al.

Lazar NA (2009) Discussion of "Puzzlingly High Correlations in fMRI Studies of Emotion, Personality, and Social Cognition" by Vul et al. (2009). Perspectives on Psychological Science 4,3:308-309.

Lieberman MD, Berkman ET, Wager TD (2009) Correlations in Social Neuroscience Aren't Voodoo: Commentary on Vul et al. (2009). Perspectives on Psychological Science 4,3:299-307.

Lindquist MA, Gelman A (2009) Correlations and Multiple Comparisons in Functional Imaging: A Statistical Perspective (Commentary on Vul et al., 2009). Perspectives on Psychological Science 4,3:310-313.

Nichols TE, Poline JB (2009) Commentary on Vul et al.'s (2009) "Puzzlingly High Correlations in fMRI Studies of Emotion, Personality, and Social Cognition". Perspectives on Psychological Science 4,3:291-293.

Poldrack RA, Mumford JA (2009) Independence in ROI analysis: where is the voodoo? Social Cognitive and Affective Neuroscience 4,2:208-213.

Yarkoni T (2009) Big Correlations in Little Studies: Inflated fMRI Correlations Reflect Low Statistical Power—Commentary on Vul et al (2009). Perspectives on Psychological Science 4,3:294-298.

Vul E, Harris C, Winkielman P, Pashler, H (2009) Reply to Comments on "Puzzlingly High Correlations in fMRI Studies of Emotion, Personality, and Social Cognition". Perspectives on Psychological Science 4,3:319-324.

Region-of-interest analysis and the use of functional localizers

Friston KJ, Rotshtein P, Geng JJ, Sterzer P, Henson RN (2006b) A critique of functional localisers. Neuroimage 30:1077-1087.

Friston KJ, Henson RN (2006) Commentary on: Divide and conquer; a defence of functional localisers. Neuroimage 30:1097-1099.

Poldrack RA (2007) Region of interest analysis for fMRI. Soc Cogn Affect Neurosci 2:67-70.

Saxe R, Brett M, Kanwisher N (2006) Divide and conquer: a defense of functional localizers. Neuroimage 30:1088-1096; discussion 1097-1089.

Conjunction analysis

Friston KJ, Holmes AP, Price CJ, Buchel C, Worsley KJ (1999) Multisubject fMRI studies and conjunction analyses. Neuroimage 10:385-396.

Friston KJ, Penny WD, Glaser DE (2005a) Conjunction revisited. NeuroImage 25:661-667.

Nichols T, Brett M, Andersson J, Wager T, Poline JB (2005) Valid conjunction inference with the minimum statistic. Neuroimage 25:653-660.

Bayesian analysis

Friston KJ, Glaser DE, Henson RN, Kiebel S, Phillips C, Ashburner J (2002) Classical and Bayesian inference in neuroimaging: applications. Neuroimage 16:484-512.

Friston KJ, Penny W, Phillips C, Kiebel S, Hinton G, Ashburner J (2002) Classical and Bayesian inference in neuroimaging: theory. Neuroimage 16:465-483.

Gossl C, Auer DP, Fahrmeir L (2001) Bayesian spatiotemporal inference in functional magnetic resonance imaging. Biometrics 57:554-562.

Neumann J, Lohmann G (2003) Bayesian second-level analysis of functional magnetic resonance images. Neuroimage 20:1346-1355.

Information-based and multivoxel pattern analysis

Haynes JD, Rees G (2006) Decoding mental states from brain activity in humans. Nature Reviews Neuroscience 7:523-534.

Kriegeskorte N, Goebel R, Bandettini P (2006) Information-based functional brain mapping. Proceedings of the National Academy of Sciences of the United States of America 103:3863-3868.

Norman KA, Polyn SM, Detre GJ, Haxby JV (2006) Beyond mind-reading: multi-voxel pattern analysis of fMRI data. Trends Cogn Sci 10:424-430.

Connectivity

Horwitz B, Warner B, Fitzer J, Tagamets MA, Husain FT, Long TW (2005) Investigating the neural basis for functional and effective connectivity. Application to fMRI. Philos Trans R Soc Lond B Biol Sci 360:1093-1108.

Ramnani N, Behrens TEJ, Penny W, Matthews PM (2004) New approaches for exploring anatomical and functional connectivity in the human brain. Biological Psychiatry 56:613-619.

Rykhlevskaia E, Gratton G, Fabiani M (2008) Combining structural and functional neuroimaging data for studying brain connectivity: a review. Psychophysiology 45:173-187.

Reporting an fMRI study

Poldrack RA, Fletcher PC, Henson RN, Worsley KJ, Brett M, Nichols TE (2008) Guidelines for reporting an fMRI study. NeuroImage 40:409-414.

Anatomy matters

Derrfuss J, Mar RA (2009) Lost in localization: The need for a universal coordinate database. NeuroImage 48: 1-7; discussion 8-20.

Devlin JT, Poldrack RA (2007) In praise of tedious anatomy. Neuroimage 37:1033-1041; discussion 1050-1038.

Tzourio-Mazoyer N, Herve PY, Mazoyer B (2007) Neuroanatomy: tool for functional localization, key to brain organization. Neuroimage 37:1059-1060; discussion 1066-1058.

Van Essen DC, Dierker D (2007) On navigating the human cerebral cortex: response to 'in praise of tedious anatomy'. Neuroimage 37:1050-1054; discussion 1066-1058.

Interpreting results from an fMRI study

Bandettini PA, Petridou N, Bodurka J (2005) Direct detection of neuronal activity with MRI: Fantasy, possibility, or reality? Applied Magnetic Resonance 29:65-88.

Goense JB, Logothetis NK (2008) Neurophysiology of the BOLD fMRI signal in awake monkeys. Curr Biol 18:631-640.

Leopold DA, Murayama Y, Logothetis NK (2003) Very slow activity fluctuations in monkey visual cortex: implications for functional brain imaging. Cereb Cortex 13:422-433.

Logothetis NK, Wandell BA (2004) Interpreting the BOLD signal. Annu Rev Physiol 66:735-769.

Logothetis NK (2007) The ins and outs of fMRI signals. Nat Neurosci 10:1230-1232.

Ritter P, Villringer A (2002) Inhibition and functional magnetic resonance imaging. Brain Activation and Cbf Control, Proceedings 1235:213-222

Stefanovic B, Warnking JM, Pike GB (2004) Hemodynamic and metabolic responses to neuronal inhibition. Neuroimage 22:771-778.

Combining fMRI with other methods

Dale AM, Halgren E (2001) Spatiotemporal mapping of brain activity by integration of multiple imaging modalities. Curr Opin Neurobiol 11:202-208.

Goldman RI, Stern JM, Engel J, Jr., Cohen MS (2000) Acquiring simultaneous EEG and functional MRI. Clin Neurophysiol 111:1974-1980.

Menon V, Crottaz-Herbette S (2005) Combined EEG and fMRI studies of human brain function. Int Rev Neurobiol 66:291-321.

Mullinger K, Debener S, Coxon R, Bowtell R (2008) Effects of simultaneous EEG recording on MRI data quality at 1.5, 3 and 7 tesla. International Journal of Psychophysiology 67:178-188.

Ritter P, Villringer A (2006) Simultaneous EEG-fMRI. Neuroscience and Biobehavioral Reviews 30:823-838.