1. DRCMR Danish Research Centre for MR fMRI –Signal, Noise and Experimental Design Torben Ellegaard Lund

2. DRCMR Danish Research Centre for MR The BOLD signal Increased neural activity leads to: Increased regional oxygen consumption (rCMRO 2 ) 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

3. DRCMR Danish Research Centre for MR The BOLD signal The three components has different time- constants and effects: The rCMRO 2 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)

4. DRCMR Danish Research Centre for MR The BOLD signal What are the optimal imaging parameters?: TE, Bandwidth, sequence type Spatiotemporal resolution/coverage Slice orientation Etc.

5. DRCMR Danish Research Centre for MR The BOLD signal T2 or T2* ?

6. DRCMR Danish Research Centre for MR The BOLD signal Which TE? S(t)=I 0 e -t/T2*

7. DRCMR Danish Research Centre for MR The BOLD signal A time course Langkilde & Rostrup

8. DRCMR Danish 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

9. DRCMR Danish Research Centre for MR 1/f Noise Suggested origins: Drift in shim and gradient currents Motion Spontaneous neural activity

10. DRCMR Danish Research Centre for MR Solutions: Fitting T2* Blocking events together 1/f Noise

11. DRCMR Danish Research Centre for MR Stimulus locked motion Examples: Swallowing Speaking Jaw clenching Tongue movement Eye movements Head movement Birn et al. HBM 1999

12. DRCMR Danish Research Centre for MR Cardiac Induced Noise When critically sampled e.g. TR=143ms Weisskoff et al. 1993

13. DRCMR Danish Research Centre for MR Aliasing When? Nyquist criterion: 2f  f s Example heart rates: 61, 74 and 91 bpm Sampled at 0.5Hz i.e. TR=2s

14. DRCMR Danish Research Centre for MR Jitter The heart rate is not constant (f s =5.4Hz)  f~0.1Hz=6bpm

15. DRCMR Danish Research Centre for MR Cardiac Induced Noise When not critically sampled e.g. TR=3000ms Hu et al. 1993 Dagli et al. 1999

16. DRCMR Danish 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

17. DRCMR Danish 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

18. DRCMR Danish 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

19. DRCMR Danish Research Centre for MR Cardiac Induced Noise Over sampled: TR=200ms Under sampled TR=1.6s -but cardiac noise is now modelled Example: Flickering checkerboard Lund et al. ISMRM 2001

20. DRCMR Danish Research Centre for MR Links SPM http://www.fil.ion.ucl.ac.uk/spm/ http://www.fil.ion.ucl.ac.uk/spm/ FSL http://www.fmrib.ox.ac.uk/fsl/index.html http://www.fmrib.ox.ac.uk/fsl/index.html SPM extensions http://www.fil.ion.ucl.ac.uk/spm/ext/ http://www.fil.ion.ucl.ac.uk/spm/ext/ DRCMR http://www.drcmr.dk/ http://www.drcmr.dk/