thank you very much
Joseph Ackerman Jr
Cell: 314-623-2605
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From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Stamatios Sotiropoulos [[log in to unmask]]
Sent: Monday, October 01, 2012 1:26 PM
To: [log in to unmask]
Subject: Re: [FSL] Topup application of generated "map"
Hi Joseph,
You do not necessarily need to have the full dataset acquired with both phase encoding directions. Once you have run topup on a single pair (or multiple pairs) of b0s you can apply the results to your dataset.
Run applytopup -h to get the help menu. You will see that there are two examples under Usage. The second is appropriate for your case (i.e. data with a single phase encoding direction). You just need to make sure that the --inindex points to an entry in acqparams.txt that refers to a b0 with the same phase-encoding direction as the data you are attempting to correct.
Cheers
Stam
On 1 Oct 2012, at 19:16, Joseph Ackerman wrote:
> I am new to Topup but have been successful at generating the "results_fieldcoef" and "results_movpar" files. The data set I am working with is a multi-volume diffusion (including b0) with positive phase-encode and a b0 with a negative phase-encoding. The hope / plan was to generate a field map type correction from topup using the two b0s since they have opposite phase encodes.
>
> Reading more of the topup and applytopup documentation it appears, and perhaps I am misunderstanding, that applytopup expects two "full" data sets, one positive and one negative, (in my case I only have one, positive) and it will use the output from topup to correct each pair of images. Is there anyway to use the output from topup without having a pair of diffusion data? Can the output be rationally used (or modified) to correct the distortions (from phase)?
>
> Thanks for any suggestions.
>
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