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Dear Jesper,

Thanks for your email.


Here are the commands we used:

# run topup
topup --imain=b0_all.nii.gz --datain=acqparams.txt
--config=${FSLDIR}/etc/flirtsch/b02b0.cnf --out=topup --iout=topup_hifi_b0

# prepare to run eddy
fslmaths topup_hifi_b0 -Tmean topup_hifi_b0
bet topup_hifi_b0 topup_hifi_b0_bet -m

# run eddy
eddy --imain=dwi_RL.nii --mask=topup_hifi_b0_bet_mask.nii.gz
--acqp=acqparams.txt --index=index.txt --bvecs=bvecs_RL.txt
--bvals=bvals_RL.txt --topup=topup --out=dwi_corrected


Please see attached for a copy of our --acqp and --index file.


Regarding PE, I have been told that it was definitely R->L and L->R, but
mri_info says "PhEncDir: UNKNOWN."


Simon


On 12 November 2015 at 18:16, Jesper Andersson <
[log in to unmask]> wrote:

> Dear Simon,
>
> >
> > We are trying to use the combination of topup and eddy to correct for
> susceptibility distortions and eddy currents/movements in our diffusion
> data. We acquired one set of volumes with phase-encoding R>>L consisting of
> 7 b=0 volumes and 60 gradient-weighted volumes. We also acquired one single
> b=0 volume with phase-encoding L>>R. The attached screenshot shows our
> diffusion data before (on the left) and after (on the right) running topup
> and eddy. In this case the uncorrected data appears to be less distorted
> than the corrected data. What might be the cause of this problem?
>
> I would need to see the commands you used and the contents of your --acqp
> and --index file to have a chance of diagnosing what went wrong.
>
> One thing though, are you certain the PE is R->L and L->R? Looking at the
> before figure it looks more like an A->P image to me. The pile up of
> intensity posterior to the ear-canals in particular makes it look like that.
>
> Jesper
>
> >
> > Kind regards,
> >
> > Simon Baker
> > Brain & Mental Health Laboratory
> > Institute of Cognitive & Clinical Neuroscience
> > Monash University
> >
> > <before_after.png>
>