Dear Adam,
eddy isn’t really designed for this type of data. The diffusion model that eddy uses internally hinges on data being acquired with multiple directions (different bvecs) on one or more “shells”. A “shell" is simply a collection of scans with the same b-value and different bvecs. Ideally those bvecs should also be designed so as to span that shell as evenly as possible.
It won’t be able to deal with the kind of data you have.
Best regards Jesper
> On 29 Jan 2020, at 17:01, Adam John <[log in to unmask]> wrote:
>
> Hello all,
>
> I use FSL 6.0.1. and I am trying to rund eddy_openmp. I successfully ran topup command without any error (two b=0 volumes AP, PA with diferent phase gradient direction).
>
> I have 4D MR DWI input data that consists of 10 volumes (10 different "b" values). Here are my parameters:
>
> text file with information about the acquisition of the images:
> 0 -1 0 0.0646
> 0 1 0 0.0646
>
> bvals: 0 10 20 30 50 100 200 500 1000 2000
>
> bvecs:
> 0 1 1 1 1 1 1 1 1 1
> 0 1 1 1 1 1 1 1 1 1
> 0 1 1 1 1 1 1 1 1 1
>
> My command line: eddy_openmp --imain=data --mask=my_hifi_b0_brain_mask --acqp=acqparams.txt --index=index.txt --bvecs=bvecs --bvals=bvals --topup=my_topup_results --out=eddy_corrected_data --data_is_shelled --verbose
>
> And here is the error message:
>
> Reading images
> Performing volume-to-volume registration
> Running Register
> Loading prediction maker
> Evaluating prediction maker model
> Calculating parameter updates
> Iter: 0, Total mss = 110.108
> Loading prediction maker
> Evaluating prediction maker model
> Calculating parameter updates
> Iter: 1, Total mss = 110.108
> Loading prediction maker
> Evaluating prediction maker model
> Calculating parameter updates
> Iter: 2, Total mss = 110.108
> Loading prediction maker
> Evaluating prediction maker model
> Calculating parameter updates
> Iter: 3, Total mss = 110.108
> Loading prediction maker
> Evaluating prediction maker model
> Calculating parameter updates
> Iter: 4, Total mss = 110.108
> Running sm.ApplyB0LocationReference
> Running Register
> Loading prediction maker
> Evaluating prediction maker model
> Estimated hyperparameters: -nan
> 0.450000
> 0.000000
> -nan
> -nan
> -nan
> -nan
>
> Calculating parameter updates
> Iter: 0, Total mss = 4277.756814
>
> error: solve(): solution not found
>
> solve(): solution not found
> EDDY::: ECScanClasses.cpp::: void EDDY::ECScanManager::SeparateFieldOffsetFromMovement(EDDY::ScanType, EDDY::OffsetModel): Exception thrown
> EDDY::: eddy.cpp::: EDDY::ReplacementManager* EDDY::Register(const EDDY::EddyCommandLineOptions&, EDDY::ScanType, unsigned int, const std::vector<float, std::allocator<float> >&, EDDY::SecondLevelECModel, bool, EDDY::ECScanManager&, EDDY::ReplacementManager*, NEWMAT::Matrix&, NEWMAT::Matrix&): Exception thrown
> EDDY::: Eddy failed with message EDDY::: eddy.cpp::: EDDY::ReplacementManager* EDDY::DoVolumeToVolumeRegistration(const EDDY::EddyCommandLineOptions&, EDDY::ECScanManager&): Exception thrown
>
> Total mss=110.108 is the same for all iterations - do you know how it is possible? It might be the problem...
>
> Please, do you have any idea what I did wrong? Unfortunately, I didn´t find any case dealing with that issue before.
> I removed a bottom slice for each volume - should I add another extra flag due to that?
>
> Thanks a lot
> Regards
> Adam
>
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