I'm working with a dataset collected on a Phillips 3T scanner, and I'm currently putting together a diffusion/TBSS pipeline. The acquisition protocol has the B0 volume collected last out of the 60 volumes (instead of first, as listed in the TOPUP userguide example). Other coworkers of mine have written scripts to split and recombine the volumes with the B0 at the front, so as to fully follow the FSL practicals and userguide, and then written further scripts to change the bvecs and bvals so the 0s are at the front of the rows vs the end.
Instead of shuffling everything around and scripting, is it an acceptable practice to extract the B0 volume using "fslroi dwidata nodif 60 1" instead of "fslroi dwidata nodif 0 1"? If I understand correctly, this would extract the B0 volume and would negate the need for to shuffle the volumes, and change the bvecs/bvals files.
Please advise if this would work, or if I am heading astray.