Some bonus thoughts after checking your protocol txt file:
- I’d set the number of points to 2048 (keep 2 kHz spectral width). Gives you a few extra data points per ppm. Keep consistent for all MRS scans.
- Acquire all scans for each region consecutively, then turn over to the other region. Don’t alternate between regions (it will trigger re-shim and re-calibration). If you give the two scans of the same region the same geometry name, it should lock their localization together (but always double-check!!).
- For the first MRS scan in each region, set
Preparation phasestofull; the second one can just be set toauto. - For MEGA-PRESS in particular, you will want to optimize the slice-selective gradient orientations to minimize out-of-voxel echoes (see thread here).
- There is a caveat to this: since you’ll be operating in cortical regions very close to the skull, you’ll want to make sure you’re not getting lipid contamination. This can be achieved by moving the voxel a few mm away from the skull or by making sure that the chemical shift displacement (denoted by the second box; set
Postproc→Shifted metabolite displayedtoLip/Lacand determined by the slice-selection gradient polarity settingsChem Shift Dir AP/LR/FH) puts the area where the lipids towards the inside of the brain. Again, make sure these settings are completely consistent for all of your scans.
- There is a caveat to this: since you’ll be operating in cortical regions very close to the skull, you’ll want to make sure you’re not getting lipid contamination. This can be achieved by moving the voxel a few mm away from the skull or by making sure that the chemical shift displacement (denoted by the second box; set
- Make sure that all of your more generic parameters are identical between MRS scans of the same region (e.g. VOI orientation once you have determined the best one).
- Very specifically, make sure that the GABA-editing settings are exactly identical between regions. The bandwidth is set to 80 Hz for one and to 100 scan for another. Choose the lowest possible value here (it’ll be around 80 Hz for TE = 68 ms).
- You can also reduce the shim size setting - I think it’s usually sufficient to add 5 mm to the voxel volume in all directions.
- I’d set
PNS modeto the highest possible value.