Hi,
I would like to ask if the magnitude_brain (betted Magnitude map) is used to mask the
4D DTI DATA when running FEAT GUI to do B0 distortion correction?
I have run a few samples on FEAT GUI to do only the B0 distortion correction on DTI data.
However, in the output folder, the only 4D DTI undistorted output available has been
bettted, and there are some area lost in the inferior temporal lobe region. I have re-
betted the Magnitude map liberally at a threshold of 0.15, before inputting the
Magnitude_brain file to run this function in the FEAT GUI. Everything is turned off in the
prestats section including the "BET brain extraction" option. However, this problem
remains. Is there any way to resolve this? or to get an undistorted 4D DTI output file that
is not already betted?
I performed tractography on the original distorted dti data and the betted undistorted dti
data, and for a few tracts from the temporal lobe, their volume is less when derived from
the betted undistorted dti, so I'm not sure if it's due to the "lost" area in the betted
undistorted dti, or the undistorted effect.
Many Thanks
Siewmin
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