Dear Lauren,
I would recommend using the same warp resolution for all subjects, just to avoid there being any registration-based bias between groups or wrt any covariates in your subsequent analysis. It is possible, for example, that certain structures might be moved into slightly different positions on average if you allow the warp more flexibility in some cases but not in others. Although this is not likely, it is worth avoid it if possible, and if you decide it is necessary to use a higher resolution warp in some cases then using that in the other cases should still give a good result.
However, we would not recommend using fnirt to register between EPI and structural images. I'm not entirely sure from your email if that is what you are doing. I hope it is not. If you are registering between the structural image and the template with fnirt, and varying the warp resolution for this, then that's fine. In that case it is separate from the EPI to structural registration (with BBR and unwarping) and you can try different options until you decide on what is best and then simply combine your adapted fnirt registration with the unwarping and registration from EPI to structural using the script "updatefeatreg". You simply copy over the registration that you want to replace from the original FEAT run (e.g., highres2standard_warp in your case) and then run this script. It will then combine everything together as if it had been run by the original pipeline.
If you are using fnirt for registering EPI to structural images then I would advise against it, as it is likely that it is shifting things in ways that are not consistent with the physics of the distortion process and therefore putting things into the wrong anatomical locations. In cases where the EPI to structural registration requires improvement, we would recommend trying different options with the fieldmaps and BBR instead.
I hope this helps.
All the best,
Mark
> On 9 Nov 2018, at 20:28, Lauren Zajac <[log in to unmask]> wrote:
>
> Hi FSL experts,
>
> I have a few specific questions about applying registrations and unwarping images. The first is whether you recommend that the same warp resolution be applied to all participants when using FNIRT to nonlinearly register EPI images to a highres structural and then to a template. I have some participants that appear to require a smaller warp resolution than others. The second question is related to when unwarping and registration are applied in FEAT and how to apply different registrations after this process. I've been running unwarping and registration through the FEAT GUI on my participants, but then have tested out lower warp resolutions on some participants after that, which I'm planning to apply. Do I have to always run the unwarping steps when I try out different warp resolutions for them to ultimately be accurate when I apply them? Thanks so much!
>
> Lauren
>
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