Hi,
Just to check - have you set the Brain/Background threshold
to 0% in the "Misc" tab on the Feat GUI?
All the best,
Mark
On 7 May 2009, at 18:40, Siewmin Gan wrote:
> 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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