FMRI Data Analysis

Old Data Analysis Guide

• Part I: Data Preprocessing
• Part II: Troubleshooting FMRI data
• Part III: Convolution and General Linear Modeling
• Part IV: Within and Between Group Analyses
• Part V: Viewing contrast data and thresholding your data
• Part VI: Region of interest analyses and dumping timecourses
• Part VII: Additional data analysis techniques
• Appendix A: AFNI Programs
• Appendix B: Detailed discussion of the process script
• Appendix C: Stats tutorial
• Appendix D: Alternatives for making regressors

Data Preprocessing and Troubleshooting

• Anatomical preprocessing (nudging and warping)
• Functional preprocessing
• Checking for motion
• Troubleshooting and artifacts
• Python batch preprocessing script

Convolution and General Linear Modeling

• Concepts and Theory
• Making regressors
• Running the general linear model (GLM)
• MSSD

Group Maps

• Group anatomical
• Group level t-tests
• Individual differences
• Making activation tables

Volume of Interest Analysis

• Making VOI Masks
• Warping VOI Masks
• Dumping Timecourses
  • Averaged Timecourse (iresp)
  • Raw Timecourses
  • Regression Coefficients
• Plotting timecourses
• Logistic regression
• Mediation Analysis

What does this AFNI Function do?

• AFNI Programs and Plugins: Scripts in the lab rely heavily on built-in functions and programs within AFNI but the usage of these functions may seem unclear. View a list of AFNI functions that gives a brief description about their usage. More information including function options can be found in the help menu within AFNI or a google search for the function name.

General Methods

• E-prime
• MATLAB
• Stata

Exercise for new neuroimagers

If you're new to FMRI data analysis I would recommend the following exercise. Find a recent neuroimaging paper (for example Knutson et. al. 2005 or Knutson et. al. 2007 would work well). First give the paper a quick read through to get the main idea of the paper. Next, slowly and carefully read through the methods section. Try to identify all of the steps required to run the analyzes in the paper. See if you can match the steps you found in the methods section to the directions available in this lab manual. This will give you a good sense of the overall process of neuroimaging analysis.