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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