Dear FSL users,
I used FLIRT to register some coronally-acquired T1s to the MNI template,
which resulted in orientations problems for s o m e of the images (for some
images the registered image appeared in the same orientation as the MNI
template, for the rest I got an interesting set of orientations. As the
images were acquired and converted with the same parameters, I would be very
interested if anybody could explain why registration worked only for some?)
Therefore, I re-oriented the images to match axial acquisition, using:
fslswapdim input_image x z y output_image.
My question: I got a left-right warning:
WARNING:: Flipping Left/Right orientation (as det < 0)
However, an anatomical landmark appeared on the same side in the axial plane
both before and after fslswap. Would I be safe to ignore the warning and
assume that left-right orientation is maintained as per original image?
(My approach will be to use fslswap to get all the coronal analyze T1 images
to the axial orientation before any further processing with FSL -bet, fast,
flirt,etc. Would there be any other recommendations on that?).
Many thanks for your invaluable help!