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fsl_prepare_fieldmap is _only_ for “traditional” fieldmaps, i.e. for the case where you have acquired dual echo-time gradient echo images.

In you case it is much more straightforward, provided the relevant acquisition parameters were the same for your “fieldmap SE-EPI images” as for your subsequent diffusion images.

You need to prepare a 4D image as input to topup. I recommend you use the b0 image from your diffusion data set as the first volume in that file, and use the “fieldmap SE-EPI” with the opposing PE-direction as the second image. That means you will not use the “fieldmap SE-EPI” image with the same PE-direction as the diffusion data.

After that you can just follow the instructions in https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup and https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/eddy. I think it will be pretty straightforward.

Jesper

On 8 Aug 2018, at 16:09, Josh Robinson <[log in to unmask]> wrote:

Matt,

Thank you for the response!

The field of view between our DTI acquisition and field map acquisition match (read=210mm, phase=100%), and both cover whole brain. Our field maps are SE EPI images collected in opposite phase encoding directions, A>P and P>A. Forgive me if this is still too vague, if you would like more detail I would be happy to share more of our acquisition privately.

Based on your response, it would seem that we can run topup with our fieldmaps and feed that into eddy, rather than using fsl_prepare_fieldmap and fugue/feat to register our field maps to our eddy-corrected b0, correct?

Your guidance is much appreciated.

Best,

Josh

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