Calculating Magnitude Images from Phasediff


For some of our participants, we did not obtain the magnitude images of the field maps from the scanner. We have the phasediff images and are wondering if there is a way to back-calculate the magnitude image from the phasediff image.

I have seen from FSL’s FUGUE that one can use fslcomplex to obtain magnitude images, but from what I am reading (Chris Rordens Neuropsychology Lab :: Fieldmaps), that seems to only work with real/imaginary images.


This figure illustrates the situation. You can use the complex data (real and imaginary) to reconstruct the scalar magnitude and the phase. Your phase difference map is not sufficient to infer the magnitude image. For Siemens scanners, it is critical to set the console to save both the magnitude and phase reconstruction.