Hi!
I am trying to undistort some EPI data that we acquired on a Bruker 7T using FUGUE.
The main problem that I have is that the output I get from FUGUE seems scrambled.
Specifically, if I do not use a mask, I get only noise. If I do use a mask, I get only zeros where the brain should be, and a nice black rectangle of zeros in all but the coronal view.
The fieldmap I have is apparently a map of differences in Hz, along with a magnitude map.
The range of differences is from about -32000 to about +32000, everything in float format.
I first multiply the fieldmap by 6.28 to get to radians per sec.
I then align the epi and the magnitude map and apply the alignment to the scaled phase difference map.
The resulting alignment looks good.
Finally, I run fugue with the following flags:
-v
-i epi.nii
--loadfmap=fieldmap.nii.gz
--unwarpdir=y
-u epi_unwarp.nii.gz
--mask=epi_mask.nii
--dwell=0.032
Is there any obvious mistake in these steps?
Has anyone successfully undistorted Bruker EPI (or DTI) data using FUGUE?
Thanks, Caspar
|