So I had a multi-shell protocol which I was supposed to start using for a new study soon. It consisted of 2 shells (b=1000, b=2000), with both shells having 64 directions, and full volumes acquired in both AP and PA directions. Voxel size 2mm isotropic.
Upon coming across fixel-based analysis, and reading the recommendation of a b value of 2500 or higher, I decided to tweak the protocol a little bit. I ended up increasing the second shell’s b value from 2000 to 2500.
After testing the new protocol, I noticed multiple voxels in the FA maps having nonsensically high FA values (>1) dispersed throughout the image. I went back to images which were acquired using the older protocol (second shell b=2000), and such voxels where almost absent (although I did find a few). I also noticed that denoising the images (as recommended in your documentation) reduced the prevalence of such voxels using both protocols.
My question is, should I be worried about the noise produced by the higher b-value (2500)? Is that what’s causing the erroneous voxels? Should I stick with the original 2 shells (b=1000, 2000)? I know the protocol is not optimal, I would ideally want less gradient directions in the b=1000 shell and more in the b=2000/2500 shell, but at this point in time I have to choose between the 2. Which one would you recommend, generally and specifically for using CSD and FBA?
Sorry for the long post, and I hope my question isn’t too amateurish. I’m a physician, so my education didn’t exactly prepare me for making these decisions, and I’m pretty much doing everything on my own. Thanks for the help!