Dear FSL Experts,
I am trying to prepare fieldmaps for FUGUE and have a problem with the prelude command where the fieldmaps dont fully unwrap.
I am using Siemens 7T data with two pahse and two magnitude images which
I can not feed into fsl_prepare_fieldmap (due to having seperate phase images), so I followed the
steps of non-siemens data.
The phase images are in radians as prescribed.
After using the proposed prelude commands:
prelude -a fieldmap_mag -p phase0_rad -o phase0_unwrapped_rad
prelude -a fieldmap_mag -p phase1_rad -o phase1_unwrapped_rad
I found, that the images are not fully unwrapped with sharp edges.
So I changed it to the following:
prelude -a fieldmap_mag -p phase0_rad -o phase0_unwrapped_rad -n 30 -m
prelude -a fieldmap_mag -p phase1_rad -o phase1_unwrapped_rad -n 30 -m
(with m being the mask from the magnitude image)
The unwrapping was still not good so I changed the n value several times,
but everytime one area that was unwrapped previously got fixed, another
showed up in a different area:
Does anyone know how to fix this?
Thank you so much for your help in advance!
Best,
Anna