Bibliography *********************************************************************
I. Web sites for analysis software.
http://www.loni.ucla.edu/AIR/
http://www.fil.ion.bpmf.ac.uk/spm http://www.biophysics.mcw.edu/BRI-MRI/afni
http://www.cmrr.drad.umn.edu/stimulate/
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II. ROI Analysis vs. Voxel-wise Analysis.
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III. Image Registration. Within-subject, within-modality: to correct for between-scan motion artifact. Within-subject, across-modality: to display brain activity on top of a structural scan, for localization. Between-subject: to account for variations in brain shape, and for standardization of localization.
Authors Method (1)Woods et al. (AIR). variance of ratios (2)Friston et al. (1995) principal warps (3)Chen, Pelizarri et al. surface matching (4)Mintun et al. zero-crossings (5)Alpert et al.,Dhawan et al. principal axes
References.
Alpert NM, Bradshaw JF, Kennedy D, Correia JA, The principal axis transformation -- a method for image registration. J Nucl Med 1990; 31:1717-22.
Collins DL, Neelin P, Peters TM, Evans AC, Automatic 3D intersubject registration of MR volumetric data in standardized Talairach space, J Comput Assist Tomogr 18(2):192-205 (1994).
Dhawan AP, Arata LK, Levy AV, Mantil J, Iterative principal axes registration method for analysis of MR-PET brain images, IEEE Transactions on Biomedical Engineering 42 (11):1079-87 (1995).
Friston KJ, Ashburner J, Poline JB, Frith CD, Heather JD, Frackowiak RSJ, Spatial registration and normalization of images, Hum Brain Mapp 2:165-189 (1995).
Friston KJ, Frith CD, Liddle PF, Frackowiak RSJ, Plastic transformation of PET images, J Comput Assist Tomogr 15:634-639 (1991).
Friston KJ, Passingham RE, Nutt JG, Heather JD, Sawle GV, Frackowiak RSJ, Localisation in PET images: direct fitting of the intercomissural (AC-PC) line, J Cereb Blood Flow Metab 9:690-695 (1989).
Minoshima S, Berger KL, Lee KS, Mintun MA, An automated method for rotational correction and centering of three-dimensional functional brain images, J Nucl Med 1992; 33:1579-1585.
Mintun MA, Lee KS, Mathematical realignment of paired PET images to enable pixel-by-pixel subtraction. J Nucl Med 1990;31:816.
Pelizzari CA, Chen GTY, Spelbring DR, Weichselbaum RR, Chen CT, Accurate three-dimensional registration of CT, PET, and/or MR images of the brain, J Comput Assist Tomogr 13(1):20-26 (1989).
Talairach J, Tournoux P, Co-Planar Stereotactic Atlas of the Human Brain, translated by Rayport M, New York: Thieme Medical Publishers, 1988.
Woods RP, Cherry SR, Mazziotta JC, Rapid Automated Algorithm for Aligning and Reslicing PET Images, J Comput Assist Tomogr 16 (4):620-33 (1992).
Woods RP, Mazziotta JC, Cherry SR, MRI-PET Registration with Automated Algorithm, J Comput Assist Tomogr 17 (4):536-546 (1993).
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IV. Spatial and Temporal Smoothing. Why is smoothing done?
(A) Matched Filter Theorem.
(B) Gaussian Random Field Theory.
References.
Holmes AP (1994):, Statistical Issues in Functional Brain Mapping, thesis submitted to the University of Glasgow for the Degree of Doctor of Philosophy, Department of Statistics. See especially section 2.1.
Poline JB, Mazoyer B, Enhanced detection in activation brain maps using a multifiltering approach, J Cereb Blood Flow Metab 14:639-641(1994).
Press WH, Teukolsky SA, Vetterling WT, Flannery BP, Numerical Recipes in C, 2nd edition, Cambridge:Cambridge University Press (1992).
Rosenfeld A, Kak AC (1982): Digital Picture Processing, Volume 2. Orlando, Fla: Academic Press, pp. 42-43.
Worsley KJ, Marrett S, Neelin P, Evans AC, Searching scale space for activation in PET images, Hum Brain Mapp , 4:74-90 (1996).
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V. Correction for Changes in Global Mean Intensity. Global changes in image intensity, often seen in PET imaging, even in apparently well-controlled setting. Sometimes can be due to experimental manipulation (sleep, procaine). Seems to be less of a problem in fMRI. ANCOVA versus ratio-normalization. Z-score normalization.
References.
Friston KJ, Frith CD, Liddle PF, Lammertsma AA, Dolan RD, Frackowiak RSJ, The Relationship Between Global and Local Changes in PET Scans, J Cereb Blood Flow Metab 10:458-466 (1990).
Holmes AP (1994):, Statistical Issues in Functional Brain Mapping, thesis submitted to the University of Glasgow for the Degree of Doctor of Philosophy, Department of Statistics. See especially section 2.1.
Van Horn JD, McIntosh AR, Maisog J Ma, Complications in the use of the SPM Chi-Squared statistic, letter to the editor, J Cereb Blood Flow Metab 15:895-896 (1995).
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VI. Analysis.
(A) Univariate statistical tests.
(1) Correlation.
(2) t-test.
(3) ANCOVA.
(4) ANOVA.
(5) Multiple Regression.
(B) Multivariate statistical tests. Principal Components Analysis. Discriminant Function Analysis. Canonical Correlations.
(C) Non-parametric approaches.
References.
Arndt S, Cizadlo T, Andreasen NC, Zeien G, Harris G, O'Leary DS, Watkins GL, Ponto LLB, Hichwa RD, A comparison of approaches to the statistical analysis of [15O]H2O PET cognitive activation studies, Journal of Neuropsychiatry and Clinical Neurosciences 7:155-168 (1995).
Bandettini PA, Jesmanowicz A, Wong EC, Hyde JS, Processing strategies for time-course data sets in functional MRI of the human brain, Magn Reson Med 30: 161-173 (1993).
Friston KJ, Jezzard P, Turner R, Analysis of Functional MRI Time-Series, Hum Brain Mapp 1:153-171 (1994).
Holmes AP (1994):, Statistical Issues in Functional Brain Mapping, thesis submitted to the University of Glasgow for the Degree of Doctor of Philosophy, Department of Statistics.
Friston KJ, Holmes AP, Worsley KJ, Poline JB, Frith CD, Frackowiak RSJ, Statistical Parametric Maps in Functional Neuroimaging: A General Linear Approach, Hum Brain Mapp 2:189-210 (1995).
Priestley MB (1981): Spectral Analysis and Time Series, San Diego: Academic Press, pp. 210-211.
Rencher AC, Methods of Multivariate Analysis, New York: John Wiley & Sons (1995), pp. 366-380.
Worsley KJ, Friston KJ, Analysis of fMRI time-series revisited - again, NeuroImage, 2:173-181 (1995).
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VII. Correction for Multiple Comparisons, Final Assessment of Significance. Need to take into account thousands of simultaneous, correlated tests.
References.
Adler RJ, The Geometry of Random Fields, New York: Wiley, 1981.
Federighi, E.T., Extended tables of the percentage points of Student's t-distribution, J. Am. Stat. Assoc., 54:683-688 (1959).
Forman SD, Cohen JD, Fitzgerald M, Eddy WF, Mintun MA, Noll DC, Improved Assessment of Significant Activations in Functional Magnetic Resonance Imaging (fMRI): Use of a Cluster-Size Threshold, Magn Reson Med 33:636-647 (1995).
Fox PT, Mintun MA, Noninvasive functional brain mapping by change-distribution analysis of averaged PET images of H215O tissue activity, J Nucl Med 30:141-149 (1989).
Friston KJ, Worsley KJ, Frackowiak RSJ, Mazziotta JC, Evans AC, Assessing the Significance of Focal Activations Using Their Spatial Extent, Hum Brain Mapp 1:210-220 (1994).
Paulson E, An approximate normalization of the Analysis of Variance distribution, Ann Math Statist 13:233-235 (1942).
Poline JB, Mazoyer B, Analysis of individual positron emission tomography activation maps by detection of high signal to noise ratio pixel clusters, J Cereb Blood Flow Metab 13:425-437 (1993).
Poline JB, Mazoyer B, Enhanced detection in activation brain maps using a multifiltering approach, J Cereb Blood Flow Metab 14:639-641(1994).
Poline JB, Mazoyer B, Cluster analysis in individual functional brain images: some new techniques to enhance the sensitivity of activation detection methods, Hum Brain Mapp 2:103-111 (1994).
Roland PE, Levin B, Kawashima R, Ēkerman S, Three-dimensional analysis of clustered voxels in 15O-butanol brain activation images, Hum Brain Mapp 1:3-19 (1993).
Worsley KJ, The geometry of random images, Chance 9(1):27-40 (1996).
Worsley KJ, Evans AC, Marrett S, Neelin P, A Three-Dimensional Statistical Analysis for CBF Activation Studies in Human Brain, J Cereb Blood Flow Metab 12:900-918 (1992).
Worsley KJ, Poline JB, Vandal AC, Friston KJ, Tests for Distributed, Nonfocal Brain Activations, Neuroimage 2:183-194 (1995).
Worsley KJ, Marrett S, Neelin P, Evans AC, Searching scale space for activation in PET images, Hum Brain Mapp , 4:74-90 (1996).