Essentials of FMRI data analysis

An intensive 7-week course on the physical basics of MR imaging, the physiology of functional MRI, and the essentials of FMRI data analysis, using 2 popular software packages, FSL and SPM.

Seminar

  1. History of Neuroimaging | Seminar PDF
  2. Basic Statistics of FMRI Data Analysis
  3. MRI Safety Instructions
  4. MRI Physics (Huettel, Song, McCarthy: Chapters 3-5) | Seminar PDF
  5. Physiological Basis of FMRI (Huettel, Song, McCarthy: Chapters 6 & 7)
  6. Signal, Noise, and Preprocessing of FMRI Data (Huettel, Song, McCarthy: Chapter 8)
  7. Experimental Design (Huettel, Song, McCarthy: Chapter 9)
  8. Statistical Analyses (Huettel, Song, McCarthy: Chapter 10)

Software Practical FSL

  1. Introduction to neuroimaging data analysis software, UNIX basics, MR image basics | Practical 1 PDF
  2. MR image display | Practical 2 PDF
  3. FMRI preprocessing | Practical 3 PDF
  4. Head motion, General Linear Model, statistical analysis | Practical 4 PDF

Required Reading

Huettel SA, Song AW & McCarthy G. Functional Magnetic Resonance Imaging. Sinauer 2009 | Table of Contents

Recommended Reading

Jenkinson M & Chappell M. Introduction to Neuroimaging Analysis. Oxford University Press 2018 | Neuroimaging Primers | Book Review

Siemens. Magnets, Spins, and Resonances. An introduction to the basics of Magnetic Resonance. | PDF English | PDF Chinese | PDF French | PDF German | PDF Spanish

Oxford Neuroimaging Primers: Recommended Example Boxes

  1. MRI artifacts
  2. Task fMRI data
  3. Brain extraction
  4. Troubleshooting brain extraction
  5. Spatial Transformations
  6. Registration
  7. Registration case studies

Recommended Web Pages

Siemens Safety Videos | Part 1 | Part 2 | Part 3