I've recently started on FSL for the first time and am currently running
bedpostx analysis on a series of DTI scans. These are producing good results
with correct orientation of fibres when FA is overlaid with V1. However,
I've noticed that the orientation of the images is R-A-I; whereas, the
orientation of the MNI152 standard images is R-P-I. Does this become
problematic for registration purposes and would it be advisable to re-orient
the DTI images to R-P-I prior to running bedpostX?
At the moment, once the bedpostx is complete, I am making a seed-point
using a high-resolution mprage image, which is also R-A-I oriented. Then,
with the registration tool of FDT diffusion, I select this mprage for the
"Main structural image" and MNI152_T1_2mm_brain for "standard space". Moving
on to the Probtrackx, selecting the str2diff matrix that the above
registration created, and running the Probtrackx produces reasonable tracts
- however, I'm unsure as to whether I'm missing a step or, again, whether or
not the fact that my DTI and mprage images are R-P-I is problematic for
Any advice would be useful.