Dear Joe,
> I am using TOPUP to correct 7T multiband collected images at 0.8mm resolution from an oblique slab. I find topup works better when the effective readout time (as read by the .json file created when converting from DICOM to NIFTI using dcm2niix) of 0.067 is used rather than the default 1.0, as you might expect. However from playing around I have noted that further decreasing this value (to say 0.005) gives even better results. I would be happy to send example images.
I don’t think there is a default value for that parameter. What I usually recommend to put (as a kind of default I guess) when people don’t know, is to use 0.05.
>
> Is there a reason this value should be kept strictly at the effective readout time, or can it be arbitarily decreased until the best results are obtained? (assessed visually).
For almost all cases it doesn’t matter what value you put. As long as the data you use to calculate the field (with warps) has been acquired with the exact same parameters as the data you plan to correct with the field, it doesn’t matter.
I am very surprised that you see a difference in performance though. It would only affect performance indirectly, through its impact on the regularisation of the field. Internally it is the off-resonance field (in units of Hz) that is regularised, so if you reduce the readout by a factor of 10 you will multiply the off-resonance field by the same factor and effectively increase the regularisation by the same factor. But my experience of topup has been that it is very robust even to large changes in the regularisation.
But I have seen very strange looking estimated fields (with strange streaks going orthogonal to the PE-direction) from _some_ multiband data, and I have never quite been able to figure out what is going on there. Maybe a dataset like that could benefit from increased regularisation. As far as I can remember it has always been Phillips data that has given those strange fields.
Jesper
>
> Best,
> Joe
>
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