Transcript Final project assignment

fMRI: Biological Basis and Experiment Design
Lecture 16: Final projects
• Experiment design
• Data simulation
• Data analysis
1 light year = 5,913,000,000,000 miles?
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)
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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
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)
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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
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
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%
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
Sample product: design and simulation
Simulated neural
activity for block
design
Simulated BOLD
responses for block
design
(optional this week)
Sample project – V1 contextual modulation
experiment
3 experimental conditions
Functional localizer to select ROI
Today: block design experiment
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
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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