Fmap 2 phase images question (fmriprep)

Hi there!
It has been awhile and we got a new scanner so we are running through our first fmriprep pipeline with the data.
Our new fieldmap outputs 2 magnitude images, and 2 phase images. To calculate the phasediff image, is it appropriate to just use fslmaths to subtract the two?

Hi @jrobinson,

The 2mag/2phase case is BIDS valid as is (described here: Magnetic Resonance Imaging - Brain Imaging Data Structure v1.9.0). The phase difference should be calculated within fMRIPrep, so no additional user intervention should be needed before preprocessing.