Hi again Ross,
>
> I am getting a very similar error message to the last poster (Nikitas); ie:
>
> EDDY::: DoVolumeToVolumeRegistration: Unable to find volume with no outliers in shell 0 with b-value=49?
> EDDY::: Eddy failed with message EDDY::: eddy.cpp::: EDDY::ReplacementManager* EDDY::DoVolumeToVolumeRegistration(const EDDY::EddyCommandLineOptions&, EDDY::ECScanManager&): Exception thrown
>
>
> This is occurring when I run eddy_cuda with slice-to-volume correction; however when I run eddy_cuda without s2v correction, there are no problems.
>
> In this dataset, I also have a small number of volumes - 6 - with low-b-value ~ 500. Does this mess with the s2v process? (No volumes with b ~ 50 - so not sure where it found that number!)
as I suspected this is an issue with not being able to find a single volume in the b=500 shell that doesn’t have at least one outlier slice. It seems that for some reason the final number it the error message is overwritten with a ?.
I can’t re-run your command here because I don’t have the "slspec_ABCD102.txt” file. Can I ask you to please re-run the s2v command with --ol_ec=2 and let me know what you get?
Jesper
>
> Just for completeness, this works:
>
> eddy_cuda9.1 --imain=input.nii.gz --mask=input_topup_unwarped_brain_mask --acqp=ABCD102_acq_param.txt --index=index_ABCD102.txt --repol --bvecs=input.bvec --bvals=input.bval --topup=input_topup_results --out=input_eddycorrected --cnr_maps --data_is_shelled
>
> and this gives the error:
>
> eddy_cuda9.1 --imain=input.nii.gz --mask=input_topup_unwarped_brain_mask --acqp=ABCD102_acq_param.txt --index=index_ABCD102.txt --repol --bvecs=input.bvec --bvals=input.bval --topup=input_topup_results --out=input_eddycorrected --cnr_maps --data_is_shelled --mporder=6 --slspec=slspec_ABCD102.txt --s2v_niter=5 --s2v_lambda=1 --s2v_interp=trilinear
>
> Thanks,
>
> Ross
>
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