1. fMRI: Biological Basis and Experiment Design Lecture 5: non-BOLD MRI Equilibrium and excitation Relaxation rates Image contrast –TE –TR

2. Equilibrium (classical picture) In free space, these spins have no preferred orientation, but in a magnetic field, they like to be aligned with the field. B0B0 No net magnetization in free space Sample has net equilibrium magnetization, M 0, in "magnet". M0M0

3. Excitation (classical picture) B0B0 Equilibrium M 0 is rotated away from positive z- axis by excitation pulse, through a flip angle, . M0M0 B0B0 Excitation M 

4. Excitation (classical picture) Magnetization vector is always described by 2 components, longitudinal and transverse. B0B0 Excitation M  MM M ||

5. Relaxation rates T 1 : longitudinal (spin-lattice) relaxation –Exchange of energy between protons and their environment –Time-scale around 1s M MM M || time

6. Relaxation rates T 1 : longitudinal (spin-lattice) relaxation T 2 : transverse (spin-spin) relaxation –Exchange of energy between protons –Time-scale ~50ms M MM M || MM time

7. Relaxation rates T 1 : longitudinal (spin-lattice) relaxation T 2 : transverse (spin-spin) relaxation T 2 *: transverse relaxation in the presence of magnetic field inhomogeneities –Bread and butter of BOLD fMRI M MM M || B0B0  "B 0 " is never perfectly uniform - macroscopic variation - microscopic variation

8. The diverse environment in a voxel Reina de la Torre et al (1998) Anatomical Record 251:87 375  m Imaging signal comes from protons on water molecules. Sensitive to microscopic variations in B 0.

9. Paramagnetic deoxygenated blood is different from diamagnetic tissue Reina de la Torre et al (1998) Anatomical Record 251:87 375  m Protons surrounded by paramagnetic environment will resonate at a slightly higher frequency (near veins with deoxyhemoglobin) Protons surrounded by diamagnetic environment will resonate at a lower frequency (when tissue and/or blood is fully oxygenated)

10. Heterogeneous magnetic field environments result in short T 2 * decay times Reina de la Torre et al (1998) Anatomical Record 251:87 375  m