drcmr danish research centre for mr fmri –signal, noise and experimental design torben ellegaard...
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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 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 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 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