Hi Leonor,
thanks very much, that’s very helpful.
I see that, in both cases, you have only one unique phase encoding direction (data_no_PE_dirs) in your acquisition parameter file (i.e., what you pass using the -par option in eddy_quad) but, in your eddy index file, you specify 2 (i.e., the second line in your acquisition parameter file) as phase encoding direction for the dataset (data_unique_pes).
I think this is what is causing the issue here. I.e., check that you have 2 unique phase encoding directions in your acqparameters file and/or change the eddy indices to 1. Happy to have a look at those two files if it helps.
Cheers,
Matteo
> On 13 Feb 2019, at 12:35, Leonor Agan <[log in to unmask]> wrote:
>
> Hi Matteo,
>
> Our datasets have:
>
> "data_no_PE_dirs": 1,
> "data_no_b0_vols": 8,
> "data_no_dw_vols": 60,
> "data_no_shells": 1,
> "data_protocol": [
> 8,
> 60
> ],
> "data_unique_bvals": [
> 1000
> ],
> "data_unique_pes": [
> 2
> ],
> "data_vox_size": [
> 2.4000000953674316,
> 2.4000000953674316,
> 2.4000000953674316
> ],
>
>
> On another dataset, we have:
>
> "data_no_PE_dirs": 1,
> "data_no_b0_vols": 14,
> "data_no_dw_vols": 120,
> "data_no_shells": 1,
> "data_protocol": [
> 14,
> 120
> ],
> "data_unique_bvals": [
> 2700
> ],
> "data_unique_pes": [
> 2
> ],
> "data_vox_size": [
> 2.4000000953674316,
> 2.4000000953674316,
> 2.4000000953674316
>
> All the best,
> Leonor
>
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