I have posted a message in the FSL mailing list concerning this topic before, but I have since then started using MRTrix as well and I wonder if the same issues apply (full existing thread begins here: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1808&L=FSL&P=R73012&1=FSL&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4).
Briefly, I am acquiring some diffusion measurements using a protocol similar to the one of the Human Connectome Project. This means that we have 4 multiband multishell diffusion acquisitions: 2 with 79 directions and 2 with 81 directions, each pair with phase encoding direction AP and PA respectively.
The issue is the following. We have discovered that our scanner facility adds at the start of every multiband scan 2 calibration b0s. There are other b0s in our acquisition, interspersed among the volumes, but these calibration volumes have particular properties. Here is the description I made in the FSL list:
Our physicist has gotten back to me with some more specifics on this calibration b0. First of all, it is worth mentioning that we are scanning with a multiband factor 4 and our TR is 3.2. The calibration b0 is reconstructed from four b0 volumes, of which each is acquired with the same TR of the other directions. Specifically, to reconstruct this volume, each multiband series of four slices is acquired 4 separate times. Therefore theoretically the SNR of this volume is sqrt(4) times higher than the b0s in the diffusion acquisition. All the other acquisition parameters, e.g. TR, TE, echo spacing etc, are the same as the other diffusion volumes, and it also has the same signal level and contrast as the other b0s.
At first, we thought of removing these calibration volumes, but this made our files incompatible with preprocessing using the HCP scripts. In the FSL mailing list, we were reassured to find out that keeping them actually does not affect preprocessing. However, Jesper from FSL suggested removing them before running bedpostx or dtifit. The thing I would like to know is, would these volumes similarly impact your implementation of multi-tissue constrained CSD and would you also recommend removing them? The preprocessing collapses all diffusion directions into one file, this is why identifying and removing these calibration b0s and modifying the bvals/bvecs accordingly could be laborious and we are wondering if it is necessary.
Thank you very much for your help.