• 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 2011 – Monday mornings from 9:00-12:00.
• Where: Gambrell 149.
• Syllabus
• Course slides: PPT Powerpoint Format.
• Textbook: Functional Magnetic Resonance Imaging by Huettel, Song, and McCarthy
• 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

• 22 Aug 2011: 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 MRIcron
• 29 Aug 2011: MRI physics: Image Acquisition.
  • Terrific videos (from a company that makes a unique instructional MRI system.
• 5 Sept: No class (labor day).
• 12 Sept 2011: 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.
• 19 Sept 2011: fMRI Paradigm Design.
  • My fMRI simulator allows you to explore the hemodynamic changes induced by different tasks.
• 26 Sept 2011: Statistics and Thresholding.
• 3 Oct 2010: 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
• 10 Oct 2011: 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
• 17 Oct 2011: Temporal Processing
  • Interactive filtering demo shows how low-pass, high-pass and notch filters modulate a signal.
  • Physiological Artifact Removal Tool
• 24 Oct 2011: Guest lecture: Event related potentials. Jennifer Vendemia
• 31 Oct 2011: 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)
• 7 Nov 2011: Detecting subtle changes in brain structure: Voxel Based Morphometry and Diffusion Tensor Imaging.
  • John Ashburner’s VBM class (PDF)
  • DTI tutorial
• 14 Nov 2011: 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
• 21 Nov 2011:Brain stimulation: Transcranial Magnetic Stimulation (TMS), Transcranial Direct Current Stimulation (tDCS). Roger Newman-Norlund and Chris Rorden
• 28 Nov 2011: Student presentations: Resting state analysis, effective and functional connectivity, independent components analysis, neural current MRI?

Relevant Links:

• 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.