Thank you for your advice. When I run eddy separately on single shells it is able to finish successfully. Does this give you any more info?I also looked at my data and I couldn't find a sign of excessive motion (signal drop out) or timing error, at least by eyeballing. Is there a more rigorous way to inspect the data?
Thank you,Mahmoud
Dear Mahmoud,
this indicates that for one of the shells eddy has not been able to find any volume without outlier slices. This could be due either to a subject that moves a lot, and that therefore has a lot of outlier slices. I have also seen it be due to small timing errors in the sequence that has led to one slice/group consistently having lower than expect intensity.
The “quick fix” is to increase slightly the threshold for threshold detection (i.e. to set --ol_nstd a little higher than the 4 default). The longer term solution is to check your data carefully to ensure you dont have timing errors.
Jesper
On 21 Jun 2019, at 01:49, Mahmoud <[log in to unmask]> wrote:
Hello,
I am re-posting my previous this again, hoping that someone can give me an answer.I get this error running eddy on some of ur subjects:
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
Aborted (core dumped)
What could be wrong? and what could be the solution?
Thank you,Mahmoud
Dear Jesper and other experts, I am running eddy_cuda on my 2-shells data. It is working well for all data but it fails on a couple of subjects. Here is the last bit of eddy_cuda output which I believe is the error message. 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 Please let me know if anyone has a solution for this. Thank you, Mahmoud
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