1. Introduction: A Brief History of fMRI, from the 1990s to the Present 2. Acquisition Parameters and Your Experiment: The Intersection of Scanning Protocols, Experimental Design, and Statistical Power 3. How to Choose which Package to use?: An Introduction to the Big Three (AFNI, FSL, and SPM), Recent Packages to be Familiar with, and the Advantages of Each 4. Determining which Programming Language to Use: Unix, Matlab, Python, and the Rise of Jupyter Notebooks 5. Standardized Data Organization and Preprocessing: The History and Uses of BIDS, fMRIPREP, and introduction to Neurodesk.org 6. Region of Interest analyses revisited: The Many Ways to Select and Analyze a Region, and the Strengths of Each Approach 7.

Pitfalls of fMRI Analysis: Circularity, Biased Analyses, and Insidious Artifacts - How You Can Best Protect Yourself and Your Data 8. Statistical Modeling and Correcting for Multiple Comparisons: The History of Univariate Analysis, a Deep Dive into Recent Developments, and What Might Work Best for You 9. New Developments in Functional Connectivity: Dynamic Connectivity, Clinical Applications, and the Connectome as a Neural Fingerprint 10. New Developments in Machine Learning: Hyperalignment, Hybrid Hyperalignment, and Clinical Uses of Representational Similarity Analysis 11. What is Open Science?: A Look into the Latest Trend of Pre-Registering Your Study, How to Share Data and Results, and What This Means for the Field 12. Large Databases, Open-Access Databases, and their Uses: Can Big Data and Meta-Analyses Ameliorate the Problems of Reproducibility? 13. Bringing It All Together: Summarizing the Main Points of This Book 14. Where do we go from here? The Future of Neuroimaging Analysis 15.

Appendix A: Review of Papers that Question fMRI Findings: Vul, Bennet Eklund, Marek, and the NARPS Paper: What to Learn from Them, and How to Keep Them in Perspective 16. Appendix B: AI and Neuroimaging Analysis - How Tools such as ChatGPT and Other Large Language Models Can Inform Preprocessing and Analysis of fMRI Data.