As long as your bvecs and bvals take into account all of your b0 volumes,
they will be included in the DTIFIT and BEDPOSTX calculations. You should
use the dti_FA for registering the image to the structural to generate a
transformation matrix, but not as the nodif_brain image.
Regarding the different acquisition plane and non-isotropic voxel size, so
long as you don't have a gap between the slices it should be fine.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Live Eikenes
Sent: Thursday, November 15, 2007 8:08 AM
To: [log in to unmask]
Subject: [FSL] nodif_brain in registration
Dear FSL users,
I have a simple question about the nodif_brain file needed for the
registration between the structural image and the diffusion image after
BedpostX and before probtrackX in Fdt:
Should the nodif_brain file only be one volume, and should it be just
one average, or all the b0 averages that I have?
I also read that the registration between the structural image and the
diffusion image becomes better when using the dti_FA image instead of
the b0 image (nodif_brain image). Should I therefore use the dti_FA as
my nodif_brain image in the BedpostX directory when applying the
registration?
Another question about the structural image is: does it matter if the
structural image is a sagital image (not isotropic, 1mm x 1mm x
1.3mm)), and that the diffusion image is an axial image?
Thank you very much!
Best regards, Live Eikenes.
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