Thanks a lot Danny for this detailed explanation. Actually this relieved me. I thought that I need to apply fslroi to extract all the b0 volumes then merge them together.
Sounds perfect!
So I need only the first b0 volume to start processing the DTI data.
Actually what I still unable to figure out is how the "dtifit" tool will work while I have non diffusion volumes reside between the diffusion volumes. Is it because the information about the vectors and b values are already recorded in bval and bvecs as you said?
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