fMRI: Biological Basis and Experiment DesignLecture 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?

Localizers scans define ROI

Sample data – selected voxels, impulse response

Subject 3

Subject 4

Subject 2

Subject 1

voxe

l

time (seconds ... scans concatenated)

Scan 1 Scan 2 Scan 3 Scan 4

Sample data – ROI average

Subject 3

Subject 4

Subject 2

Subject 1

voxe

l

time (seconds ... scans concatenated)

Scan 1 Scan 2 Scan 3 Scan 4

Sample data – response average (60 trials)

Subject 3

Subject 4

Subject 2

Subject 1

time (seconds)

Sample data – response average (30 trials)

Subject 3

Subject 4

Subject 2

Subject 1

time (seconds)

Sample data – response average (15 trials)

Subject 3

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Subject 2

Subject 1

time (seconds)

Effect of averaging

Subject 3

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Subject 2

Subject 1

NM

Error bars are S.E.M. (M)

Analyzing each scan separately

Subject 3

Subject 4

Subject 2

Subject 1

Baselines and contrasts

20s block cycles 10s block cycles

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

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 (1/8th volume)– for the sake of argument:

• SNRthermal,3mm = 160

• SNRthermal,1.5mm = 20

SNRthermal: block and ER design

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

2.10083.0

01.0

3.70083.0

06.0

ER

ERER

block

blockblock

N

CCNR

N

CCNR

2.10083.0

01.0

ER

ERER N

CCNR3.7

0083.0

06.0

block

blockblock N

CCNR

Response estimate: single voxel (SNR = 120)

Sample data – block experiment

Scan 2Scan 1

time (seconds ... 2 scans concatenated)

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ROI average predicted from HIRF

Block response estimated with different HIRFsHIRF HRF