Hi,
try:
--resamp=lsr
(and possibly --fep)
in your eddy call.
Cheers,
Andreas
Am 06.10.17, 00:20 schrieb "FSL - FMRIB's Software Library on behalf of
Edouard Mior" unter <[log in to unmask] on behalf of [log in to unmask]>:
>Hi FSL experts,
>
>I'm processing the connectome DWI images for a study. I have two
>sequences (AP and PA) with 79 directions.
>In each sequences (AP and PA) I have 6 b0 images distributed across all
>79 directions, not just acquired at the beginning.
>
>I'm trying to integrate a solution to our pipeline process for dealing
>with such datas.
>
>What is the best way, using fsl tools ( topup, eddy) , to correct
>(distortion, eddy-current) those datas ?
>
>
>Currently I'm doing:
>
>1 - extract all b0s from the two sequences
>2 - merge all b0s (so 12 in total) into one single 4D volume
>3 - use topup to create the distortion map and the text file
>4 - create a brain mask
>5 - merge my two AP/PA sequences into one 4D volume , so I have in one
>sequence 158 volumes.
>6 - use eddy with the recommended parameters
>
>but at the end I have a file with 158 vol and not 79 as expected.
>
>I would like to have, at the end, just one corrected 4D volume with
>79dir.
>
>
>thank you,
>
>Edouard.
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