Dear MRtrix team,
In our lab, we are looking into optimizing our dwi acquisition to be able to perform FBA in ex vivo rat brain data.
We have tried a couple of different approaches, but are unsure how to decide which approach is optimal for what we want to achieve.
As mentioned, we want to perform FBA (to determine e.g. Apparent Fiber Density), since we are interested in WM tracts in the midbrain and brain stem (which contain many crossing fibres).
We have the possibility for scanning time up to 36 hours (over the weekend) on a 9.4T system. We are using a multishot EPI sequence.
- Regarding voxel size, we used to acquire our data with voxels of 150um isotropic, but have been playing around with smaller voxel sizes even (62.5um isotropic).
- Regarding b-values, since we used 600, 1200, 1800 and 2400 in vivo, we thought to use 1500, 3000, 4500 and 6000 ex-vivo (since I read in another topic that your team recommended the b-values to be 3-4 times higher ex-vivo).
- We have 110 diffusion-weighted directions.
From what I understand, more directions, higer b-values and smaller voxel size are better to resolve crossing fibers issues, but high b-values and small voxel size also affect SNR. We do have the scanning time to acquire at 62.5um isotropic, but is it worth it with the SNR trade-off?
My questions are: (1) How do we determine if we should go to 62.5um isotropic or 150um isotropic? (2) Based on what I’ve described above, do you have other advise to optimize the acquisition?