OK. Thanks a lot for your answer. I used a larger input data set (more different “b” values) and it´s working. However, there is another error I still can´t overcome. I know you are not a FSL member but I don´t have any response from the FSL team yet and moreover, I haven´t found any problem simmilar to my… Please, could you have a look at my problem? Have you already encoutered with this problem?

Here is my question from the FSL forum:

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…

I removed a bottom slice for each volume - should I add another extra flag due to that?

Thanks a lot for your time

Regards

Adam