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Hi Matt, Thank you for the reply! I ran this by our physicist. Would you be able to comment on why spin echo is preferred and not gradient echo for Topup/ApplyTopup with our data? As noted, we acquired two series of images with opposite phase encoding directions (A>P, P>A); these were identical other than the phase encoding. Both were gradient echo. Thank you for your time and input, Erin > ---------------------------------------------------------------------- > > Date: Sat, 19 Jan 2019 00:00:36 +0000 > From: "Glasser, Matthew" <[log in to unmask]> > Subject: Re: topup and motion correction > > Motion correction ‹> Topup/Applytopup (computed from spin echo, not > gradient echo data) ‹> Registration to structural ‹> Temporal noise > cleanup. > > Matt. > > On 1/18/19, 3:11 PM, "FSL - FMRIB's Software Library on behalf of Erin W." > <[log in to unmask] on behalf of [log in to unmask]> wrote: > > >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 > > > > > >*********** > >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 > > ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1