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Dear experts I have a Philips DWI dataset with acquisition parameters: single band, 50 slices, ascending, 102 directions, multishell. I receive the following error with eddy (cuda: fsl 5.0.11) for "few" subjects. eddy_cuda --imain=dwi.nii --mask=mask.nii --acqp=eddy_config.txt --index=eddy_indices.txt --bvecs=bvecs --bvals=bvals --topup=field --repol --niter=6 --fwhm=10,0,0,0,0,0 --data_is_shelled --cnr_maps --residuals --mporder=18 --slspec=myslspec.txt --s2v_niter=5 --s2v_lambda=5 --s2v_interp=trilinear --out=dwi_post_eddy ...................Allocated GPU # 0................... eddy: msg=ECScanManager::set_slice_to_vol_reference: ref index out of bounds terminate called after throwing an instance of 'EDDY::EddyException' what(): eddy: msg=ECScanManager::set_slice_to_vol_reference: ref index out of bounds When I run the command without the slice to vol correction part, i.e., eddy_cuda --imain=dwi.nii --mask=mask.nii --acqp=eddy_config.txt --index=eddy_indices.txt --bvecs=bvecs --bvals=bvals --topup=field --repol --niter=6 --fwhm=10,0,0,0,0,0 --data_is_shelled --cnr_maps --residuals --out=dwi_post_eddy it finishes without error but I do see in the dwi_post_eddy.eddy_outlier_report text file that slice no.1 is an outlier in a lot of volumes. So I guess that this is the problem and for the moment I can get around the error generated above by increasing the --ol_nstd=8. I was wondering whether this the correct approach or whether I should take another approach. If this is the correct approach, should I repeat this new setting for "all" my subjects in the dataset? Another issue is the myslspec.txt file. Here is the content of myslspec.txt file: 0,1,2,3,.....49. I wonder whether it should start from zero (as it is now) or 1? Best, Hamed