Dear Jeni,
> I'm trying to do the fieldmap correction with Fugue following the online tutorial. Essentially I have a pair of the magnitude images each acquired at a different TE, and a phase difference map (our scanner is a Siemens Magnetom Trio). After checking the field map data description in the FSL documentation, I think the difference map we have is a real field map image, so I simply scaled it to rad/s. Now, in the FEAT interface where I run FUGUE, I'm not sure which magnitude image I should use in the "Fieldmap mag" entry since I have 2 of them. Could you help clarify? Thank you in advance!
It really doesn't matter since it is only used for creating a mask. Pick one, or take the sum of both.
J
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