• Title: “Neuroimaging: from image to inference”.
• Instructor: Chris Rorden :: Office 227 Discovery I
• Course Code: PSYC 888Y, 3 credits. In addition, scientists are free to audit this course. Suitable for faculty, post-docs, PhD students and advanced undergraduate students.
• When: Fall Semester 2012 – Tuesday/Thursday mornings from 8:00-9:15.
• Where: Sloan 103.
• Syllabus
• Course slides: PPT Powerpoint Format.
• Textbook: Functional Magnetic Resonance Imaging by Huettel, Song, and McCarthy

. Also suggested Handbook of Functional MRI Data Analysis by Poldrack, Mumford and Nichols.

• Description: Functional magnetic resonance imaging is a recent and powerful tool for inferring brain function. This technique identifies brain regions that are activated by different tasks – for example we can find the brain regions that activate when someone sees a familiar face. This course is designed to give students an understanding of the potential and limitations of this technique, and the ability to critically evaluate the inferences that can be drawn from fMRI. The course describes all stages of an fMRI study – from the design of the behavioral task (e.g. asking the participant to view faces), to the image processing (e.g. correcting images for head movements that occurred during scanning), through to statistical analysis (identifying brain regions that are activated by a task).

Lectures

• Overview.
  • After this class, each student should ensure they can run FSL and MRIcron on a computer. MRIcron runs on Linux, Windows and OSX. Individuals with OSX and Linux computers can install FSL natively, or students can use the provided DVD to run a NeuroDebian VirtualBox, with instructions here.
• MRI physics: Image Acquisition.
  • Terrific videos (from a company that makes a unique instructional MRI system.
• MRI physics: Image Contrast.
  • The virtual MR program allows you to interactively adjust MRI parameters and see the results.
  • Graphs (and Matlab scripts) for basic MRI contrast effects.
• fMRI Paradigm Design.
  • My fMRI simulator allows you to explore the hemodynamic changes induced by different tasks.
• Statistics and Thresholding.
• Spatial Processing I: Spatial Registration – realignment (motion correction), coregistration, normalization; Spatial interpolation – linear, spline, sinc functions
  • Spatial Processing Demos
  • Spatial Processing Videos and SPM8 scripts
• Spatial Processing Continued II: Smoothing – filters, edge detection, gaussian blur, homogeneity correction (for EPI and anatomical scans), motion related intensity changes.
  • Undistorting fMRI EPI data using the SPM FieldMap toolbox
• Temporal Processing
  • Interactive filtering demo shows how low-pass, high-pass and notch filters modulate a signal.
  • Physiological Artifact Removal Tool
• FSL and SPM. Hands on demonstrations
  • fMRI analysis
    • FSL: block design
    • FSL: event-related design
    • SPM: block design
    • SPM: event-related design
  • Automated analysis with SPM (same data as block design tutorial)
• Detecting subtle changes in brain structure: Voxel Based Morphometry and Diffusion Tensor Imaging.
  • John Ashburner’s VBM class (PDF)
  • DTI tutorial
• Brain injury and neuroimaging. Measuring blood flow and using lesion symptom mapping to understand the consequences of stroke and other neurological disorders.
  • Arterial Spin Labeling using ASLtbx
  • Contrast-enhanced (Gadolinium) Perfusion Weighted Imaging
  • VLSM using my NPM software
• Brain stimulation: Transcranial Magnetic Stimulation (TMS), Transcranial Direct Current Stimulation (tDCS). Roger Newman-Norlund and Chris Rorden
• Student presentations: Resting state analysis, effective and functional connectivity, independent components analysis, neural current MRI?

Class Schedule Fall 2012

1. Th 8/23
2. Tu 8/28
3. Th 8/30
4. Tu 9/4
5. Th 9/6
6. Tu 9/11
7. Th 9/13
8. Tu 9/18
9. Th 9/20
10. Tu 9/25
11. Th 9/27
12. Tu 10/2
13. Th 10/4
14. Tu 10/9
15. Th 10/11
16. Tu 10/16
17. Th 10/18 Fall Break – no classes
18. Tu 10/23
19. Th 10/25 guest lecture: Jessica Green: ERPs and fMRI
20. Tu 10/30
21. Th 11/1
22. Tu 11/6 General Election Day – no classes
23. Th 11/8 guest lecture: Roger Newman-Norlund: Transcranial Magnetic Stimulation (TMS)
24. Tu 11/13
25. Th 11/15
26. Tu 11/20 guest lecture: Rutvik Desai: Meta-analyses in cognitive neuroscience (target article)
27. Th 11/22 Thanksgiving recess – no classes
28. Tu 11/27
29. Th 11/29
30. Tu 12/4
31. Th 12/6 Student Presentations

Relevant Links:

• Online MRI course
• SPM statistics
• Rik Henson’s fMRI mini-course
• Rik Henson’s tips for fMRI design
• Duke BIAC Grad Course
• SPM course, and the SPM8 manual
• NeuroDebian virtual machine is a great way for students to try out neuroimaging tools.
• Lin4Neuro is an open source Linux distribution that comes with many of the most popular free MRI tools (FSL, MRIcron, etc) already installed. Simply burn a CD and reboot your computer. Release notes and other details are here. Kiyotaka Nemoto has graciously included the sample dataset from this course and the tutorial web pages, making it a perfect package for teaching brain imaging (as all the students have the datasets preloaded and in the same folders). For details, read the Lin4Neuro Article inBMC Medical Imaging article.