Hi again,
I just realized that the option --slspec is not available for eddy_openmp.
Based on the usermanual I understood that I need to use that option in order to specify the slice order when using --repol for multiband.
My scans are multiband with factor 2 and 66 slices.
The slice order is
0 33
2 35
4 37
6 39
8 41
...
32 65
1 34
3 36
...
27 60
29 62
31 64
Should I just use --mb=2 instead of slspect?
eddy_openmp --imain=rawdata_all --mask=brain_mask.nii.gz --acqp=acquisition.txt --index=index.txt --bvecs=bvecs_all --bvals=bvals_all --topup=topup_output --out=eddy_data --data_is_shelled --repol --ol_type=gw --mb=2 -v
Many thanks again for the help,
Marina
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