Not sure, I generate the white matter mask directly from the surface in
Caret. Does the white matter surface look good in FreeSurfer, i.e. does it
line up with what you see in the T1 volume?
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Francisco Costela
Sent: Friday, October 16, 2009 7:11 AM
To: [log in to unmask]
Subject: Re: [FSL] WM mask with DTIFIT?
Thanks Steve and Matt. I tried the WM mask in DTIFIT with a Philips dataset
and it worked perfectly.
I repeated the process with a Siemens dataset but I got a FA (red in the
right brain in the attached image) that is not covering the whole
WM (blue in the image).
I also applied DTIFIT with a BET brain mask to the same dataset and obtained
a correct FA (left brain).
Any idea about why this incomplete FA is being obtained using the WM mask?
Cheers,
Francisco
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