Hi Abid
nope, you shouldn't have to, as long as the header info is correct. Does it
come up properly in freeview? That is, does what freeview thinks the
orientations are match what they really are?
cheers
Bruce
On Wed,
24 Jul 2019, Abid Qureshi wrote:
External Email - Use Caution
Dear Freesurfer,
Does my T1 MPRAGE need to be in a particular orientation prior to running
recon-all? Meaning should I use mri_convert to change to RAS orientation to
avoid any L/R confusion with the output measures.
For instance, mri_info says the orientation:
MPRAGE = LPS
orig.mgz = LIA
T1.mgz = LIA
I'm confused because if you bring up an image in freeview, say the T1.mgz,
it uses the RAS coordinate system.
Thanks,
Abid
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