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fMRI: Biological Basis and Experiment Design Lecture 16: Final projects

This lecture covers the components of final projects, including abstract, background, methods, results, and discussion. It also discusses building blocks for the final project and group projects.

lewisbeverly
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fMRI: Biological Basis and Experiment Design Lecture 16: Final projects

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  1. fMRI: Biological Basis and Experiment DesignLecture 16: Final projects • Experiment design • Data simulation • Data analysis 1 light year = 5,913,000,000,000 miles?

  2. Basic assignment, final project(all projects need these components) • Abstract (250 words) • Background - experiment design and neuroscience question motivating the experiment (1 page, 1 - 3 references) • Methods (2 – 4 pages) • MR Methods section (resolution, TR, TE, protocol) • Prediction of neural activity • Prediction of BOLD response (noiseless model) • Simulated data (BOLD + noise - physiological and/or thermal) • ROI selection • GLM • Results (1 – 3 pages) • Paragraph describing simulation output + 1 figure • Paragraph describing GLM results + 1 figure • Discussion (1 - 2 pages) • 3 things that might not be as expected if you ran the experiment

  3. Building blocks, final project(weekly assignments, 2nd half of semester) • Abstract (250 words) • Background - experiment design and neuroscience question motivating the experiment (1 page, 1 - 3 references) • Methods (2 – 4 pages) • MR Methods section (resolution, TR, TE, protocol) – WA 8 • Prediction of neural activity – WA7 • Prediction of BOLD response (noiseless model) – WA7 • Simulated data (BOLD + noise - physiological and/or thermal) – WA8 • ROI selection – WA10 • GLM – WA11 & WA12 • Results (1 – 3 pages) • Paragraph describing simulation output + 1 figure – WA8 • Paragraph describing GLM results + 1 figure – WA11 & WA12 • Discussion (1 - 2 pages) • 3 things that might not be as expected if you ran the experiment

  4. Final projects: group effort • Self-organizing groups • 1 – 4 people per group • Group names submitted with experiment design, WA7 (Mar. 28) • Goes without saying – share the work equally • Any group member should be able to answer questions about any part of the project

  5. Group presentations • May 2 and May 4: 3 – 4 presentations each day • 10 min. presentation + 10 min. discussion • Sample format: • 1 person presents design • 1 person presents simulation • 1 person presents analysis • Grading criteria: • Individual's apparent contribution – 20% • Group preparation/coordination for presentation – 10% • Group project meets all requirements – 65% • Background and design – 20%; Simulation – 20%; GLM – 20%; discussion – 5% • Superior product: 5%

  6. Weekly assignment 7 • Identify group, if you're working in a group • Each group member turns in a document; all group members names are listed • Describe (2 – 3 sentences) experimental question • Can be collaborative effort • Describe (4 – 6 sent. or bullet pts.) experimental design • Functional localizers? • Block or event-related designs? • How many different stimulus conditions? • Simulate neural and BOLD activity in one voxel (similar to WA6) • Submit code and figure

  7. Sample product: design and simulation Simulated neural activity for block design Simulated BOLD responses for block design (optional this week)

  8. Sample project – V1 contextual modulation experiment 3 experimental conditions Functional localizer to select ROI Today: block design experiment

  9. Experiment design: psychophysics predicts that neural response to targets will be lower in b) than c). Stimulus presentation (block paradigm) • Each scan = 10 x 36s = 6 min. • 9 scans per session (3 each condition) is about max. or 18 s = 6 - 9 2AFC trials … or

  10. Simulated "brain" (10 x 10 array of "voxels") Simulated block response, target alone Simulated block response, target + facilitative flankers Simulated block response, target + suppressive flankers

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