To get the b0:
fslroi data nodif 0 1
To get the mask:
bet nodif nodif_brain -m -f 0.5
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Alexander Lebedev
Sent: Monday, March 30, 2009 7:04 PM
To: [log in to unmask]
Subject: [FSL] Some questions about DTI analysis
Dear FSL users. Excuse me for disturbing you. I have some questions
about dti data analysis in FDT toolbox.
Now I have 4d nii file with (+ 2 txt's: b-values and gradient
directions) getting after the convertation process from 299 dicom files
(12+1 directions)
I have finished the eddy current correction (reference vol: 0) process
and now I'm starting the "DTIfit"
I use the b0 image (raw, not corrected) as a nodif_brain_mask (is it
ok?). And could you give me advice how could I correctly get 3d mask
image from 4d nii? (It is probably due to my lack of experience...
Sorry)
And... There are many extra-brain signals in my FA-maps getting after
the processing... Is it ok?
P.S.: I've found the worm ("Scano.F") in the "FSL practicals" (3rd
archieve)...
--
Thank you beforehand
Best Regards
Alexander Lebedev.
