Greetings,
I am following up on this older inquiry. Our research group has also collected two volumes with opposite phase encoding directions and a colleague recommended we use Topup/ApplyTopup in this manner for distortion correction on our fMRI (task) data. Presently, we employ motion correction (ICA-AROMA, which requires FSL preprocessing in FEAT) and nuisance regression (WM/CSF) on 4D data. We have had conflicting recommendations on when to apply Topup/ApplyTopup. Can these tools be used prior to motion correction and nuisance regression, or should we be using them after? If after, I assume we will need to rerun registration?
Thank you for your time and input,
Erin
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Dear Ian,
> Hello,
>
> I would like to use topup to correct distortions for fMRI data. Before each run, I collected two volumes with opposite phase encoding directions. Each volume of all runs were collected with the same phase-encode direction. My protocol so far has been to merge the two volumes with opposite phase encoding, run topup on this 4D file, and then use applytopup to apply the this to the the main imaging data:
>
> topup --imain=both_b0 --datain=acqparams.txt --config=b02b0.cnf --out=topup_results
>
> applytopup --imain=<path to new BOLD scan> --inindex=1 --datain=acqparams.txt --topup=topup_results --out=<path to output name> --method=jac
>
> My question is whether this procedure will account for motion in the 4D functional data. Based on reading the documentation, it seems like maybe motion is only accounted for in volumes that are inputs to topup (in my case, motion between the first two phase encoding volumes). In that case, should I run motion correction prior to applying topup?
yes, for now you need to run motion correction first.
Jesper
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