Just to clarify, since you mention both denoising as well as gibbs ringing removal: what happens if you don’t run either the denoising, or the gibbs ringing removal? I.e., can you easily figure out which one of these steps causes the subsequent problems you’re describing? I’m asking because…
…this sounds to me as if you experience the issues when both denoising and gibbs ringing removal had been run, but not if both had not been run. So it might be useful to know what happens in the scenario just one of both (either denoising, or gibbs ringing removal) is run.
Apart from the issues, which would preferably be figured out properly and solved of course, about this though:
In my personal experience, denoising has never been crucial to the result of fixel based analyses that I have run or observed. There might be very particular scenarios where it may have a more substantial effect on the outcome of the FBA as a whole, but that would then probably be a scenario where you’re very close to e.g. your p-value threshold or similar…
Personally, I do value gibbs ringing removal a bit more (“relatively speaking”), since there’s scenarios where that can cause outright biases, even false positives, or other issues with interpretation.
All that said, I should again emphasise that it’d of course be better to figure out the true cause of the issue, so you can simply run both denoising and gibbs ringing removal without worries.