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