I have run fmriprep version 1.5.4 and am checking the html output file. Things mostly look good, but I used fieldmaps and also a magnitude fieldmap and there are some weird lines on the fieldmap magnitude image in the HTML output. When I look at both the fieldmap image, the magnitude image, and the fieldmap corrected BOLD image…they look OK. I’ve attached the image. Let me know if anyone else has seen something like this, and if you have an idea of what it might be caused by!!
That definitely looks off, on the surface this looks like a bug with that report section. Have you run other subjects, and if so, is this a persistent problem?
And if you wouldn’t mind, could you open an issue on the github repo that generates this figure?
Hi @being_saige, that fieldmap actually looks good!
So those “rays” coming out of the brain are just the extrapolation FSL FUGUE does along the PE axis to ensure that susceptibility correction does not introduce artificial cuts, tearing apart signal at locations with strong inhomogeneity gradients.
I agree it is not the most beautiful plot, and it still requires a fair bit of work (e.g., units?) but I think it clearly conveys how correction will operate.