I see.
It should be fine to keep the volumes in the original order as long as the bvals and bvecs reflect that same order (which they should).
You can just take the first b0 volume to derive nodif, nodif_brain, and nodif_brain_mask and be able to run dtifit or bedpostx.
For eddy_correct, if for some reason your first b0 volume is not suitable as reference, you can always specify your second b0 or third b0 etc to be reference:
eddy_correct original_dti corrected_dti #refnum, where #refnum can be 0, 10, 20, 30, in your case.
Best,
Danny Kim
On 2015-09-22, at 12:05 PM, Jon Anderson wrote:
> Thanks Danny
> In order to start the preprocessing steps for the DTI data. I wanted to merge the b0 volumes together and the diffusion data together.
>
> But the problem is that between every 10 diffusion data volumes I have one non diffusion. Is it enough for to use one volume b0 for preprocessing DTI data instead of merging all the b0 together?
>
> Thanks again
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