Spin echo sequences eliminate the signal dropout present in gradient echo images that will confuse the topup registration algorithm.  I suppose you could give it a try with your current data if you have no other way of doing distortion correction, but spin echo is the recommended approach.

Matt.

From: Erin Walsh <[log in to unmask]>
Date: Tuesday, January 22, 2019 at 1:55 PM
To: FSL - FMRIB's Software Library <[log in to unmask]>, Matt Glasser <[log in to unmask]>
Subject: Re: topup and motion correction

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

 

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