DRCMRDanish Research Centre for MR

fMRI –Signal, Noise and Experimental Design

Torben Ellegaard Lund

DRCMRDanish Research Centre for MR The BOLD signal

Increased neural activity leads to: Increased regional oxygen consumption

(rCMRO2) Increased regional cerebral blood flow (rCBF) Increased regional cerebral blood volume

(rCBV)

A decrease in the deoxyhaemoglobin concentration leads to a signal

increase in T2 and T2* weighted images

DRCMRDanish Research Centre for MR The BOLD signal

The three components has different time-constants and effects:

The rCMRO2 increase leads to a fast but small signal decrease known as: ”The initial dip” (1s)

The rCBF increase leads to the peak which usually dominates the haemodynamic response function (6s)

The rCBV increase leads to a signal undershoot.(12s)

DRCMRDanish Research Centre for MR The BOLD signal

What are the optimal imaging parameters?:

TE, Bandwidth, sequence typeSpatiotemporal resolution/coverageSlice orientation Etc.

DRCMRDanish Research Centre for MR The BOLD signal

T2 or T2* ?

DRCMRDanish Research Centre for MR The BOLD signal

Which TE?

S(t)=I0e-t/T2*

DRCMRDanish Research Centre for MR The BOLD signal

A time course Langkilde & Rostrup

DRCMRDanish Research Centre for MR Noise

There are several other things than the BOLD signal which vary during a fMRI time course:

Drift in shim and gradient currents (1/f noise) Cardiac pulsation Respiration Swallowing Head motion Eye movement Stimulus locked motion

DRCMRDanish Research Centre for MR 1/f Noise

Suggested origins: Drift in shim and gradient currents Motion Spontaneous neural activity

DRCMRDanish Research Centre for MR

Solutions: Fitting T2* Blocking events

together

1/f Noise

DRCMRDanish Research Centre for MR Stimulus locked motion

Examples: Swallowing Speaking Jaw clenching Tongue movement Eye movements Head movement

Birn et al. HBM 1999

DRCMRDanish Research Centre for MR Cardiac Induced Noise

When critically sampled e.g. TR=143ms

Weisskoff et al. 1993

DRCMRDanish Research Centre for MR Aliasing

When? Nyquist criterion:

2f fs

Example heart rates: 61, 74 and 91 bpm Sampled at 0.5Hz

i.e. TR=2s

DRCMRDanish Research Centre for MR Jitter

The heart rate is not constant (fs=5.4Hz)

f~0.1Hz=6bpm

DRCMRDanish Research Centre for MR Cardiac Induced Noise

When not critically samplede.g. TR=3000ms

Hu et al. 1993

Dagli et al. 1999

DRCMRDanish Research Centre for MR Cardiac Induced Noise

GLM regressors: Paradigm and 5 vessel

time series (per session) F-test:

Null-hypothesis: No effect of vessel time series

p<0.05 corrected

Lund et al. ISMRM 2002

DRCMRDanish Research Centre for MR Cardiac Induced Noise

GLM regressors: Paradigm and 5 vessel

time series (per session) F-test:

Null-hypothesis: No effectof vessel time seriesp<0.05 corrected

Lund et al. ISMRM 2002

DRCMRDanish Research Centre for MR Cardiac Induced Noise

Significant effect of nuisance covariates in: Areas surrounding

branches of the medial-, posterior and anterior cerebral arteries

Ventricles The dural venous

sinuses

Lund et al. ISMRM 2002

DRCMRDanish Research Centre for MR Cardiac Induced Noise

Over sampled: TR=200ms

Under sampled TR=1.6s

Under sampled TR=1.6s-but cardiac noise is now modelled

Example: Flickering checkerboard

Lund et al. ISMRM 2001

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