Dear Jay,
no, that is correct. Each input volume will give you two output volumes. The “least-squares reconstruction” of one output image from two input images (as available in topup) isn’t yet part of the released version of eddy. It is in our internal version so so will be available in later FSL releases. So instead each image is corrected separately using Jacobian modulation.
For now you can either average output images with the same diffusion gradient, or just use both as input to bedpost.
Jesper
On 14 Jul 2014, at 14:49, SUBSCRIBE FSL Jay <[log in to unmask]> wrote:
> Hello FSL experts,
>
> I have 2 DWI acqusitions (one B0 and 30 DWI) acquired in opposite phase encoding directions. I tried to use eddy for this data set using the following command
>
> eddy --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
>
> --imain=data consists of concatenated DWI volumes (merged AtoP and PtoA volumes)
> --acqp=acqparams.txt consists of two rows (0 -1 0 0.1; 0 1 0 0.1)
> --index=index.txt consists of series of 1's (31 times) followed by series of 2's (31 times)
> --bvecs=bvecs --bvals=bvals consists of 62 lines (first 31 lines represent bvecs,bvals for first volume, second 31 lines represent bvecs,bvals for second volume)
> topup=my_topup_results consists of the ouput generated by topup.
>
> when i view --out=eddy_corrected_data it contains 62 volumes and not 31 volumes.
> I was expecting one eddy corrected volume as an output from --out=eddy_corrected_data.
>
> Can you please tell me where am i going wrong.
> Best
> Jay
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