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.
https://drive.google.com/open?id=0BwbKkBtmWbwkYU92S2ExU1hmRmc
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:
https://drive.google.com/open?id=0BwbKkBtmWbwkVERwbmhyYXBwM3c
https://drive.google.com/open?id=0BwbKkBtmWbwkck5TVzI3OUQxUm8
https://drive.google.com/open?id=0BwbKkBtmWbwkNVdDc0FUX3dNQ2s
Does anyone know how to fix this?
Thank you so much for your help in advance!
Best,
Anna
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