Preparatory Material


Introduction to Neuroimaging and FSL

Introductory Lecture (2 videos)


Introduction to UNIX

Practicals (5 video walk-throughs)

Practical Data



Main Course Material


Section 1: Image Registration and Distortion Correction

Section 1 Pre-Practical Video

Section 1 Practical Instructions (written)

1. Introduction to Brain Extraction and Registration

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2. Registration: Image Spaces and Spatial Transformations

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3. Registration: Cost Functions, Interpolation and Masks

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4. Registration: Single Stage and Multi-Stage Applications

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5. Registration: EPI Distortion Correction and Registration

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6. Registration: Pathological Image Registration and Small FOV

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7. Segmentation: FAST

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8. Segmentation: Subcortical Brain Structures and FIRST

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9. Segmentation: White Matter Hyper-intensities and BIANCA

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10. Segmentation: Structural Analysis using FSL VBM and SIENA

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Section 3: Statistics & Task fMRI: Basic GLM and Single-Subject Analysis

Section 3 Pre-Practical Video

Section 3 Practical Instructions (written)

11. FMRI1: Introduction to Task FMRI Experiments and Analysis

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12. FMRI1: Preprocessing

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13. FMRI1: Introduction to Single Session Analysis and GLM Basics

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14. FMRI1: Modelling and Statistics

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Section 4: Statistics & Task fMRI: Inference and Group Analysis

Section 4 Pre-Practical Video

Section 4 Practical Instructions (written)

15. FMRI2: Group Analysis, Fixed/Mixed Effects, FLAME and OLS

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16. FMRI2: Examples of Group FMRI Analysis

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17. FMRI2: Multi-Session Analysis and Covariates

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18. FMRI2: Inference, Null Hypothesis Testing, and Multiple Comparisons

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19. FMRI2: Inference - Quantifying Surprise in Imaging

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20. FMRI2: Parametric Vs. Non-parametric Tests

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21. FMRI2: Threshold Free Cluster Enhancement and False Discovery Rate

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Section 5: Statistics & Task fMRI: Advanced GLM and Noise Correction

Section 5 Pre-Practical Video

Section 5 Practical Instructions (written)

22. FMRI3: Pipeline Overview

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23. FMRI3: Advanced Preprocessing

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24. FMRI3: Demeaning EVs

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25. FMRI3: Advanced Analysis, Parametric Designs

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26. FMRI3: Advanced Analysis, Factorial Designs and Interactions

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27. FMRI3: Advanced Analysis, Correlation of EVs and Design Efficiency

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Section 6: Resting-State fMRI: ICA and Dual Regression

Section 6 Pre-Practical Video

Section 6 Practical Instructions (written)

28. Resting State: Introduction to Resting State FMRI and ICA

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29. Resting State: Independent Component Analysis

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30. Resting State: Single Subject ICA

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31. Resting State: Multi-Subject ICA and Dual Regression

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Section 7: Resting-State fMRI: Network Analysis with FSLNETS

Section 7 Pre-Practical Video

Section 7 Practical Instructions (written)

32. Resting State: Preprocessing

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33. Resting State: Network Modelling Analysis, Node Definition and Edge Calculation

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34. Resting State: Network Modelling Analysis, Group Analysis and Challenges

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35. Resting State: Comparison of Resting State Methods

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Section 8: Diffusion: Diffusion Tensor Imaging and TBSS

Section 8 Pre-Practical Video

Section 8 Practical Instructions (written)

36. Diffusion 1: Tour of DTI in FSL

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37. Diffusion 1: DTI Basic Principles

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38. Diffusion 1: Tract Based Spatial Statistics (TBSS)

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39. Diffusion 2: Distortion and Movement Correction

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40. Diffusion 2: Distortion and Movement Correction 2

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41. Diffusion 2: Distortion and Movement Correction 3

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Diffusion 2: Extra Slice (Eddy Advanced Features)

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42. Diffusion Tractography: Goals of Tractography

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43. Diffusion Tractography: Estimating Fibre Orientations: BEDPOSTX

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44. Diffusion Tractography: Probabilistic Tractography: PROBTRACKX

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45. Diffusion Tractography: PROBTRACKX Outputs

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46. Diffusion Tractography: Tractography Limitations

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