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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