Dear Samuel,
are you sure it is not a brightness/contrast/scaling setting issue? It looks like the image is scaled from -30.000, and that definitely isn’t right.
Also, for future reference, you should always aim to use one of the config files we supply when running topup. So, instead of manually specifying --subsamp, --fwhm and --warpres you specify --config=b02b0.cnf, and all of that will be taken care of for you in a way that has been tried and tested.
Jesper
> On 9 May 2018, at 08:08, Samuel Holly <[log in to unmask]> wrote:
>
> Dear FSL community,
>
> I have been trying to use TOPUP to correct distortions in my DTI dataset.
>
> Everything runs well, the --iout images are less distorted than before TOPUP, however they are unusually faint (screenshot attached). This is not an issue with the brightness/contrast settings. Wiht the same brightness/contrast settings the input --imain images look normal.
>
> Here is the command I used:
>
> topup --imain=AP_PA_b0 --datain=acq_par.txt --iout=AP_PA_b0_unwarp --out=topup_results --subsamp=4,2,1 --fwhm=8,4,0 --warpres=8,6,6 -v
>
> My acq_par.txt file contains the following:
>
> 0 -1 0 0.09044
> 0 1 0 0.09044
>
> When I try to use the fieldmap from topup with eddy, the images are again less distorted, but faint as the above example.
>
> Could you kindly advise what could be going wrong and/or how to solve this?
>
> Thank you and best regards
>
> Samuel
> <faint_b0_unwarp.png>
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