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What are we measuring in fMRI?

This overview provides an explanation of the physics behind fMRI and how it is used to measure neural activity. Topics covered include the physics of the BOLD signal, the effects of magnetic fields and pulses, and the correlation of fMRI with other measures of neural activity. The implications for cognitive studies are also discussed.

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What are we measuring in fMRI?

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  1. What are we measuring in fMRI? Marieke Schölvinck

  2. Overview • Physics of BOLD signal • Magnetic fields and pulses • Magnetic properties of oxygen in blood • How we use this to generate a signal • Physiology of BOLD signal • How neurons cause blood flow increases • Implications for cognitive studies • Correlation with other measures of neural activity

  3. It all starts with hydrogen… physics magnetic dipole moment (MDM) • MDMs align with / against uniform magnetic field Bo • small % more alignwith Bo net magnetization

  4. So what goes on in the scanner? So what goes on in the scanner? physics • Place hydrogen nuclei (brain) in a uniform magnetic field (scanner) • Apply radiofrequency (RF) pulse, normally at 90° to magnetic field. This ‘tips’ MDMs of hydrogen nuclei • MDMs of hydrogen nuclei are now at 90° to main field (z), i.e. in x,y plane • Terminate RF pulse and let nuclei relax: MDMs return to original (z) orientation; energy released during relaxation is measured by receiver coil

  5. Phase physics • BEFORE the RF pulse: MDMs are not in phase • DURING the RF pulse: MDMs in phase  strong signal in x,y plane • AFTER the RF pulse: MDMs begin to dephase  signal decays • Two reasons for this dephasing: • inhomogeneities in the magnetic field • ‘spin-spin’ interactions between neighbouring nuclei

  6. Time to relax… physics • time course for MDMs to return to original (z) orientation • time course of breakdown of magnetization in the x,y plane due to spin-spin interactions • Different tissues have different T1 and T2 relaxation rates • time course of breakdown of magnetization in the x,y plane due to inhomogeneities in the magnetic field T1 relaxation T2 relaxation T2* relaxation BOLD…

  7. We measure O2 ratios in blood physics • BOLD (Blood Oxygenation Level Dependent) contrast: measures inhomogeneities in magnetic field due to changes in the level of O2 in the blood • deoxyhaemoglobin = magnetic! oxyhaemoglobin = not magnetic! So we can use the change in fMRI signal to infer the relative oxygenation of the blood! Low ratio deoxy:oxygenated blood  slow decrease in MRI signal High ratio deoxy:oxygenated blood  fast decrease in MRI signal

  8. Summary of the physics physics • MDMs of hydrogen nuclei align to magnetic field in scanner • RF pulse causes them to spin, in phase, in x,y plane • Once pulse has stopped they fall back to direction of magnetic field, dephasing as they do so • Dephasing takes various amount of time, depending in part on inhomogeneities in magnetic field • Inhomogeneities are caused by variable ratio of deoxygenated : oxygenated blood • Assumption: activity in brain area lowers this ratio and thereby decreases speed of decay of MRI signal

  9. What causes BOLD? physiology The purpose of the increase in blood oxygenation is to feed neurons… …so, what makes a neuron hungry? (neurons can’t store much energy) …and how does this change the blood flow?

  10. Hungry brains Pre-synaptic neuron physiology 2K 3Na 2K 3Na ATP ATP GLN 50-75% of energy use is action potential driven; remainder is spent on housekeeping ATP GLU + 3Na GLUTAMATE + H + K + Most energy is spent on the reuptake of glutamate and reversing ion movements! Na 2K + + Ca 2 Na 3Na ATP Glial cell Post-synaptic neuron

  11. Vascular density physiology Vascular density is proportional to synaptic density

  12. Active control of blood flow physiology

  13. Neural activity  BOLD: complicated! physiology No easy relationship going from neural activity to BOLD Relationship cannot only differ between brain area and level of activation, but also between subjects

  14. … so what does it imply? physiology • No summation of BOLD signal! • No directly comparing different areas… • Different vasculature • Different neuromodulatory control • Different circuitry BOLD [X] > BOLD [Y] does NOT mean neural activity [X] > activity [Y]!

  15. What BOLD does not measure physiology • Output of an area • Comparisons of activity between areas • Inhibitory synapses (GABA) What BOLD does (presumably) measure • Excitatory synaptic activity (input to an area) • Local processing (reuptake of glutamate) • Changes in neuromodulatory substances

  16. What does a blob in area X mean? physiology • X has changed its local activity • Change of inputs arriving at X

  17. Other ways to measure neural activity physiology Kim et al 2004

  18. Summary of the physiology physiology • Most energy is spent locally on synaptic processes • Blood flow is controlled by monoamines • BOLD does not measure output of an area, comparisons between areas, or inhibitory connections • Instead, BOLD measures changes in local activity and changes in input to an area • BOLD signal is most closely correlated with LFP signal

  19. References Physics: • Lipton ML (2007) MRI Physics: Understanding the Basics. Springer Verlag • Weishaupt et al (2003) How Does Mri Work? An Introduction to the Physics And Function of Magnetic Resonance Imaging. Springer Verlag Physiology: • Logothetis NK et al (2001) Neurophysiological investigation of the basis of the fMRI signal. Nature 412:150-157 • Attwell D & Iadecola C (2002) The neural basis of functional brain imaging signals Trends in Neurosciences 25:621-625 • Kim DS et al (2004) Spatial relationship between neuronal activity and BOLD functional MRI NeuroImage 21:876-885

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