Re: [Freesurfer] T1 orientation prior to running recon-all

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:

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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