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Hi Jesper,

Piggybacking on your email; is eddy superior to eddy_correct even if you're
just using it for basic motion correction (i.e. without any geometric
distortion correction via TOPUP)?

Thanks,
Iain

On Thu, 20 Jun 2019, 11:11 Jesper Andersson, <[log in to unmask]>
wrote:

> Dear Baixiong,
>
> you might also want to consider using eddy instead of eddy_correct. It is
> a new(er) tool that performs considerably better than eddy_correct.
>
> Jesper
>
>
>
> Hi Baixiong,
>
> Assuming that you properly ran DTIFIT between eddy_correct and your
> calculation of RD (L23) to get your diffusion maps, then I'd agree that all
> makes sense.
>
> (I'm less familiar with fslroi to extract volumes from a 4D dataset
> though; you might find fslselectvols to be more intuitive if you're only
> wanting to grab one volume from a 4D dataset).
>
> Iain
>
> On Wed, 19 Jun 2019, 12:30 Baixiong Xiao, <[log in to unmask]>
> wrote:
>
>> Dear all,
>>
>> I installed version fsl6.0. I preprocessed DTI data using the following
>> scripts: is that right? is that enough?
>>
>> fslroi  MS01.nii.gz b0 0 -1 0 -1 0 -1 0 1
>> Bet2 b0.nii.gz nodif_brain –m –f 0.3
>> eddy_correct MS01.nii.gz data 0
>> Get L23: fslmaths L2_image -add L3_image -div 2 L23
>>
>> Best
>>
>> Baixiong
>>
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