Re: [Freesurfer] recon-all: making sure that brain.mgz will be in RAS orientation.

Hi Noam

if you want your outputs in a specific coordinate system, why not just run recon-all, then mri_conver to whatever orientation you want? Internally we have a consistent orientation that you can't easily change

cheers Bruce On Sat, 9 Mar 2019, Peled, Noam wrote:

Dear group, I ran recon-all on a T1 nii file, which is in LAS orientation. The brain.mgz turn out to be in LIA orientation. I've tried to convert the nii file to RAS (mri_convert --in_orientation LAS --out_orientation RAS ...), and rerun recon-all, but it didn't change the results. How do I make sure my output files will be in RAS orientation?

Thanks, Noam