Dear Manuel,
>
> Attempting to separate field-offset from subject movement
> Running sm.ApplyShellShapeReference
> 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
>
> The command line used is:
>
> eddy_cuda7.5 --imain=8102-CONC --mask=8102-topupBET_mask --acqp=eddy_config.txt --index=eddy_indices.txt --bvecs=8102-CONC.bvec --bvals=8102-CONC.bval --repol --topup=field --out=8102-eddy --data_is_shelled --ol_type=both --mporder=7 --s2v_niter=10 --s2v_lambda=5 --slspec=8102-slspec.txt --very_verbose
I have had a look at your data now, and I have found the reason for the crash. As I indicated earlier the crash happens in a piece of code that tries to determine what volumes in each shell are best to use as “shape reference”, i.e. volumes that have not been affected by intra-volume movement.
The first thing it does is to rule out any volumes that eddy has detected outliers in (since these are a sign of movement). But it doesn’t check that there is at least one volume in each shell without outliers, and in your data there is a shell where every volume has outliers. I will add that check so that in the future it will crash with a more meaningful error message when this happens.
I will follow up this email with an email outside the mailbase where I explain more what I have seen in your data, and suggest what you can do about it in this case.
Jesper
>
> Any clue about the error? Thanks in advance.
>
> Regards,
>
> Manuel
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