Signal to noise ratio (SNR) and data quality

1. Signal to noise ratio (SNR) and data quality

2. Coils • Head coil • homogenous signal • moderate SNR • Surface coil • highest signal at hotspot • high SNR at hotspot Source: Joe Gati

3. Calculating Signal:Noise Ratio Pick a region of interest (ROI) outside the brain free from artifacts (no ghosts, susceptibility artifacts). Find mean () and standard deviation (SD). Pick an ROI inside the brain in the area you care about. Find  and SD. e.g., =4, SD=2.1 SNR = brain/ outside = 200/4 = 50 Alternatively SNR = brain/ SDoutside = 200/2.1 = 95 (should be 1/1.91 of above because /SD ~ 1.91) When citing SNR, state which denominator you used. e.g.,  = 200 Head coil should have SNR > 50:1 Surface coil should have SNR > 100:1 Source: Joe Gati, personal communication

4. What affects SNR?Physical factors Source: Doug Noll’s online tutorial and Jody Culham’s web site

5. What affects SNR?Physiological factors Source: Doug Noll’s online tutorial and Jody Culham’s web site

6. Physiological Noise • Respiration • every 4-10 sec (0.3 Hz) • moving chest distorts susceptibility • deep breaths particularly problematic • (instruct subject well) • Cardiac Cycle • every ~1 sec (0.9 Hz) • pulsing motion, blood changes • Solutions • gating • avoiding paradigms at those frequencies

7. Low and High Frequency Noise

8. Head Motion: Main Artifacts Head motion Problems • Rim artifacts • hard to tell activation from artifacts • artifacts can work against activation  time1 time2 Playing a movie of slices over time helps you detect head motion Looking at the negative tail can help you identify artifacts • 2) Region of interest moves • lose effects because you’re sampling outside ROI

9. Head Restraint • Other: • Thermoplastic Mask (used in PET) • Vacuum packs • Tape across forehead • Foam padding Head Vise (more comfortable than it sounds!) Bite Bar (less comfortable than head vice!)

10. Motion Correction Options • 2D realignment • fast • 2 degrees of freedom (2 translations) • 3D realignment • slow • more accurate • 6 degrees of freedom (3 translations, 3 rotations) • can lose parts of brain • Can realign within a run or within a session

11. Motion Correction Output SPM output raw data gradual motions are usually well-corrected linear trend removal abrupt motions are more of a problem (esp if related to paradigm motion corrected in SPM Caveat: Motion correction in BV doesn’t seem nearly as good as SPM Caveat: Motion correction can cause artifacts where there were none

12. Stationary Head Phantom • Bag of Saline on a Stick • experimenter moves saline left and right every 20 sec without touching subject or phantom Head Motion: Susceptibility Artifacts Analyze data using saline motion as “paradigm” or

13. Solution: • one trial every 10 or 20 sec • fMRI signal is delayed ~5 sec • distinguish true activity from artifacts • Especially good for motor paradigms – any artifact from the movement made by the subject should be gone once the critical data is collected! action activity fMRI Signal 0 5 10 Time (Sec) Head Motion: Solution to Susceptibility artifact

14. Effect of Filtering – spatial smoothing. before after Source: Brain Voyager course slides

15. Trial-to-trial variability Single trials Average of all trials from 2 runs

16. Other Artifacts Ghosts Zebra Brains Metallic Objects (e.g., hair tie) Spikes

17. Other Artifacts Poor shimming