Dear Jason,
I had a look at your data, and the first things that struck me was that your pixel dimensions were 1e10 mm in all directions, and that surely threw topup off. I used fsledithd to change that to 1 mm, and also fixed a malformed sform/qform (though I am not sure if the latter is necessary).
I then had a little play with topup. I started with the b02b0_1.cnf file and made some changes to that. One necessary change is to set --estmov to 0 for all levels. This is because you only have a few slices, and any out-of-plane movement that topup infers will lead to loss of a slice.
There was some limited success, but I suspect part of the problem is that it looks like one of your images is left-right flipped compared to the other. It is a little hard to say because of the distortions, but it looks to me that the middle row of 7 objects group as 4 -- 3 in one of the images and as 4 -- 3 in the other.
I suggest you take a look at that (the flip), make sure that you get pixel-dimensions right and look out for malformed sform/qform. Once you have fixed that you can start playing based on the jason.cnf config file that I have attached (it would mainly involve changes to the lambda parameter). I am afraid I don't have time to do that myself before Xmas.
I should also say that even though I think it is possible to tweak a config file for topup to work with these data, it is not ideal for what you need. Your problem is in many ways a lot easier in that you are not looking for a 3D off-resonance field. You are really only looking for a 1D profile that should then be applied to each line in the frequency encode direction. I would certainly be possible to use "topup-style" principles to write a software that finds that 1D profile, but adapting topup to that would not be easy.
Jesper
> On 9 Dec 2020, at 08:16, Jason Stockmann <[log in to unmask]> wrote:
>
> Thank you Jesper, it's very generous of you to offer to look at the files. I have included the topup_params also, although I don't know exactly what value to use for the readout duration. I was experimenting with this, but it never had any effect on the output image, which made me suspicious I had set up my NIFTI files wrong. Most of the metadata in the NIFTI is missing or dummy data.
>
> 'both_dir' was created from 'neg' and 'pos' using fslmerge.
>
> I also ran these commands first:
>
> unix('fslroi temp_pos pos 0 1')
> unix('fslroi temp_neg neg 0 1')
>
> You are correct that I am trying to correct for distortion in the readout direction, since there is a lot of gradient nonlinearity in this direction. The distortion is quite dramatic in the images. I do have a field map, and I have played with FUGUE in the past for doing this, but I wanted to try TOPUP because I have a suspicion it will be more robust.
>
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