Functional MRI User's Guide Michael A. Yassa ● The Division of Psychiatric Neuroimaging ● ● Department of Psychiatry and Behavioral Sciences ● ● The Johns Hopkins School of Medicine ● ● Baltimore, MD ● 1 Document written in OpenOffice.org Writer 2.0 by Sun Microsystems Publication date: June 2005 (1st edition) Online versions available at http://pni.med.jhu.edu/intranet /fmriguide/ Acknowledgments: This document relies heavily on expertise and advice from the following individuals and/or groups: John Ashburner, Karl Friston, and Will Penny (FIL-UCL: London), Kalina Christoff (UBC: Canada), Matthew Brett (MRC-CBU: Cambridge), and Tom Nichols (SPH-UMichigan, Ann Arbor). Some portions of this document are adapted or copied verbatim from other sources, and are referenced as such. Supplemental Reading: Frackowiak RS, Friston K, Frith C, Dolan RJ, Price CJ, Zeki S, Ashburner J, & Perchey G (2004). Human Brain Function, 2nd edition, Elsevier Academic Press, San Diego, CA. Huettel SA, Song AW, McCarthy, G. (2004) Functional Magnetic Resonance Imaging. Sinaur Associates, Sunderland, MA. 2 Table of Contents Magnetic Resonance Physics..............................................................................6 How the MR Signal is Generated.............................................................................6 The BOLD Contrast Mechanism..............................................................................8 Hemodynamic Modeling.........................................................................................10 Signal and Noise in fMRI........................................................................................12 Thermal Noise.......................................................................................................12 Cardiac and respiratory artifacts............................................................................12 N/2 Ghost..............................................................................................................12 Subject motion.......................................................................................................12 Draining veins........................................................................................................13 Scanner drift..........................................................................................................13 Susceptibility artifacts............................................................................................13 Experimental Design...........................................................................................14 Cognitive subtractions ...........................................................................................14 Cognitive Conjunctions...........................................................................................14 Parametric Designs................................................................................................14 Multi-factorial Designs............................................................................................15 Optimizing fMRI Studies.........................................................................................15 Signal Processing..................................................................................................15 Confounding Factors.............................................................................................15 Control task............................................................................................................16 Latent (hidden) factor.............................................................................................16 Randomization and Counterbalancing...................................................................16 Nonlinear Hemodynamic Effects............................................................................16 Epoch (Blocked) and Event-Related Designs .......................................................17 Spatial and Temporal Pre-Processing...............................................................18 Overview................................................................................................................18 Raw Data ...............................................................................................................18 Getting Started.......................................................................................................18 Requirements.........................................................................................................19 Hardware Requirements........................................................................................19 Software Requirements.........................................................................................19 Software Set-up......................................................................................................19 The SPM Environment...........................................................................................20 Data Transfer from Godzilla...................................................................................20 Volume Separation and Analyze headers .............................................................21 Buffer Removal.......................................................................................................24 Slice Timing Correction (For event-related data)...................................................24 To Correct or Not to Correct..................................................................................24 Philips Slice Acquisition Order...............................................................................25 Which Slice to Use as a Reference Slice...............................................................25 Timing Parameters.................................................................................................26 Rigid-Body Registration (Correction for Head Motion)...........................................26 3 Creating a Mean Image.........................................................................................26 Realignment...........................................................................................................27 Anatomical Co-registration (Optional)....................................................................29 Co-registering Whole Brain Volumes.....................................................................30 Co-registering Partial Brain Volumes.....................................................................30 Spatial Normalization to Standard Space..............................................................30 Correcting Scan Orientation..................................................................................31 Normalization Defaults...........................................................................................31 Normalization to a Standard EPI Template............................................................32 Gaussian Smoothing.............................................................................................33 Summary of Pre-processing Steps........................................................................34 Statistical Analysis using the General Linear Model.......................................35 Modeling and Inference in SPM.............................................................................35 Model Specification and the SPM Design Matrix ..................................................35 Setting Up fMRI Defaults.......................................................................................36 Model Specification................................................................................................36 Estimating a Specified Model................................................................................39 Global Intensity Normalization................................................................................40 Temporal Filtering...................................................................................................40 Results and Statistical Inference............................................................................42 Contrast Specification............................................................................................42 Thresholding and Inference ..................................................................................43 Rejecting the Null Hypothesis.................................................................................43 Type I Error (Multiple Comparison Correction).......................................................44 Spatial Extent Threshold (Cluster analysis) ...........................................................46 Viewing Results using Maximum Intensity Projection ...........................................46 Small Volume Correction and Regional Hypotheses.............................................48 Extracting Results and Talairach Labeling.............................................................48 Time-Series Extraction and Local Eigenimage Analysis .......................................49 Plotting Responses and Parameter Estimates......................................................50 Anatomical Overlays..............................................................................................53 Editing, Printing and Exporting SPM output...........................................................55 Region of Interest (ROI) Analyses......................................................................56 Anatomical vs. Functional