1. fMRI: Biological Basis and Experiment Design Lecture 17: Baselines, SNR & CNR Visualizing data Trial triggered average Baselines SNR and CNR –Block vs. ER 1 light year = 5,913,000,000,000 miles?

2. Localizers scans define ROI

3. Sample data – selected voxels, impulse response Subject 3 Subject 4 Subject 2 Subject 1 voxel time (seconds... scans concatenated) Scan 1Scan 2Scan 3Scan 4

4. Sample data – ROI average Subject 3 Subject 4 Subject 2 Subject 1 voxel time (seconds... scans concatenated) Scan 1Scan 2Scan 3Scan 4

5. Sample data – response average (60 trials) Subject 3 Subject 4 Subject 2 Subject 1 time (seconds)

6. Sample data – response average (30 trials) Subject 3 Subject 4 Subject 2 Subject 1 time (seconds)

7. Sample data – response average (15 trials) Subject 3 Subject 4 Subject 2 Subject 1 time (seconds)

8. Effect of averaging Subject 3 Subject 4 Subject 2 Subject 1 Error bars are  S.E.M. (  M )

9. Analyzing each scan separately Subject 3 Subject 4 Subject 2 Subject 1

10. Baselines and contrasts 20s block cycles10s block cycles

11. Trade-off between CNR and block length 20s block cycles, 40 repetitions 10s block cycles, 80 repetitions More contrast, fewer samples Less contrast, more samples

12. Signal-to-noise ratio Thermal noise –white –independent of voxel size –independent of tissue type –independent of voxel location –trivial with 3 x 3 x 3mm voxels –a problem with 1.5 x 1.5 x 1.5 mm voxels (1/8 th volume) –for the sake of argument: SNR thermal,3mm = 160 SNR thermal,1.5mm = 20

13. SNR thermal : block and ER design

14. Contrast-to-noise ratio: block and (slow) ER design

15. Response estimate: single voxel (SNR = 120)

16. Sample data – block experiment Scan 2 Scan 1 time (seconds... 2 scans concatenated) voxel ROI averagepredicted from HIRF

17. Block response estimated with different HIRFs HIRFHRF