🌀 Signal lost and recovered
Watch spins fall out of step, then bring part of the signal back with an echo.
Spins seen from above, turning with the field
Signal size (length of the sum)
Solid: current settings. Faint: the same with the deoxyhemoglobin switch the other way. Dotted: the T2 limit.
Press "Excite and watch".
The deoxyhemoglobin effect is exaggerated about ten times so you can see it; in real BOLD the signal changes by about 1 %.
How to read this
- After the RF pulse all spins point the same way, so their sum (the thick arrow) is long: a big signal.
- Dephasing: each spin feels a slightly different field, so each turns at a slightly different speed and they fan out. The sum shrinks: that is T2* decay. Two things cause it: fixed field differences across the voxel (from tissue, air nearby and deoxyhemoglobin in vessels) and random interactions between molecules (T2).
- Spin echo: a 180° pulse at TE/2 flips every spin to the mirror position. The fast ones are now behind, the slow ones ahead, and at TE they line up again: the fixed-field part of the loss is undone. The random T2 part is not, so the echo can never be taller than the dotted T2 limit.
- More deoxyhemoglobin adds field differences around vessels, so gradient-echo signal fades faster. Most of that is refocused by a spin echo; what is left comes from water moving (diffusing) through the uneven fields around the smallest vessels.
Why it matters: most fMRI uses gradient-echo EPI, which keeps the whole BOLD effect (bigger signal change, but also from larger veins). Spin-echo BOLD is weaker but more specific to small vessels near the active tissue, which is why it is used at 7 T for fine detail.
Values used: T2 = 90 ms and T2* = 66 ms, close to grey matter at 3 T; with the switch on, T2* = 52 ms and T2 = 85 ms.
Key terms
- Dephasing
- Spins falling out of step because they turn at slightly different speeds.
- T2
- Signal loss from random interactions between molecules; can't be undone.
- T2*
- Total signal loss: T2 plus the loss from fixed field differences in the voxel. Always shorter than T2.
- Echo time (TE)
- When the scanner reads the signal after the excitation pulse; for BOLD, about the T2* of grey matter.
- Gradient echo
- A sequence with no 180° pulse; sensitive to T2*, the usual choice for BOLD.
- Spin echo
- A sequence with a 180° pulse that refocuses fixed field differences; sensitive mainly to T2.
Sources
- Hahn E. L. (1950). Spin echoes. Physical Review 80(4): 580–594.
- Huettel S. A., Song A. W., McCarthy G. (2014). Functional Magnetic Resonance Imaging, 3rd ed., chapters 3, 5 and 7. Sinauer.
- Uludağ K., Müller-Bierl B., Uğurbil K. (2009). An integrative model for neuronal activity-induced signal changes for gradient and spin echo functional imaging. NeuroImage 48(1): 150–165.
Used in lessons 3, 9 of fMRI from zero.