Hi,

I have 3 questions and was wondering if anybody could help me out please:
1) I have multi-shell DTI data and I had read that FSL's DTIFIT tool isn't ideal for processing this kind of data that has multiple b-values (please see attached image and site: https://fsl.fmrib.ox.ac.uk/fslcourse/201... for source info). However, when I ran it on my data, it somehow did produce FA maps, etc. All I need to know is whether anybody has a good detailed understanding about the background process that FSL performs in order to generate these results and how it exactly did that for my data???
2) Secondly, with respect to the same data, when I tried performing topup on it, it gave me the error: 'Topup: msg=topup_clp::topup_clp: Mismatch between b0_all and acqparams.txt' and I checked my acquisition paramters for the original dti nifti and it said that the phase enconding direction was: j- which I assume means it is A>>P encoded, correct?? The total readout time was 0.038625 so my acqparams looks like this: 0 -1 0.038625
3) Point-2 brings me to my third question: for topup, we merge A>>P (b0 image) and P>>A; how does one get the P>>A image? Is it supposed to be in the raw data I received from the scanner itself or is it something one generates (if so, how)?
I also came across a prebaked topup tool but am confused as to whether this is a file that needs to be downloaded first.
Any and all help would be highly appreciated.
Thank you for your time.
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