Download - Signal to noise ratio (SNR) and data quality
Signal to noise ratio (SNR) and data quality
Coils
Source: Joe Gati
Head coil•homogenous signal•moderate SNR
Surface coil•highest signal at hotspot•high SNR at hotspot
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.
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)
Head coil should have SNR > 50:1
Surface coil should have SNR > 100:1
When citing SNR, state which denominator you used.
Source: Joe Gati, personal communication
e.g., =4, SD=2.1
e.g., = 200
What affects SNR?Physical factors
PHYSICAL FACTORS SOLUTION & TRADEOFFThermal Noise (body & system) Inherent – can’t change
Magnet Strengthe.g. 1.5T 4T gives 2-4X increase in SNR
Use higher field magnet– additional cost and maintenance– physiological noise may increase
Coile.g., head surface coil gives ~2+X increase in SNR
Use surface coil– Lose other brain areas– Lose homogeneity
Voxel sizee.g., doubling slice thickness increases SNR by root-2
Use larger voxel size– Lose resolution
Sampling time Longer scan sessions– additional time, money and subject discomfort
Source: Doug Noll’s online tutorial and Jody Culham’s web site
What affects SNR?Physiological factors
PHYSIOLOGICAL FACTORS SOLUTION & TRADEOFFCardiac and respiratory noise Monitor and compensate
– very difficult to do
Head (and body) motion Use experienced or well-trained subjects– limited subject pool
Use head-restraint system– subject discomfort
Post-processing correction– often incompletely effective
Single trials to avoid body motion
Low frequency noise Use smart designPerform post-processing filtering
BOLD noise (neural and vascular fluctuations) Use many trials to average out variability
Behavioral variations Use well-controlled paradigmUse many trials to average out variability
Source: Doug Noll’s online tutorial and Jody Culham’s web site
Physiological NoiseRespiration• 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
Low and High Frequency Noise
Head Motion: Main ArtifactsHead motion Problems
time1 time2
1) Rim artifacts• hard to tell activation from artifacts• artifacts can work against activation
2) Region of interest moves•lose effects because you’re sampling outside ROI
Looking at the negative tail can help you identify artifacts
Playing a movie of slices over time helps you detect head motion
Head Restraint
Head Vise(more comfortable than it
sounds!)
Bite Bar(less comfortable than head vice!)
Other:• Thermoplastic Mask (used in PET)
• Vacuum packs
• Tape across forehead
• Foam padding
Motion Correction Options2D 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
Motion Correction Output
gradual motions are usually well-corrected
abrupt motions are more of a problem (esp if related to paradigm
SPM output
raw data
linear trend removal
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
Head Motion: Susceptibility Artifacts
Stationary Head Phantom
Bag of Saline on a Stick• experimenter moves saline left and right every 20 sec without touching subject or phantom
or Analyze data using saline motion as “paradigm”
Head Motion: Solution to Susceptibility
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!
0 5 10
Time (Sec)
fMRISignal
action
activityartifact
Effect of Filtering – spatial smoothing.
before
after
Source: Brain Voyager course slides
Trial-to-trial variabilitySingle trials
Average of all trials from 2 runs
Other Artifacts
Ghosts Zebra Brains
Spikes
Metallic Objects (e.g., hair tie)
Other ArtifactsPoor shimming