Hey Bruce. Originally this is what I did. I used mri_convert on the relevant nii files, but I was wondering what to do with the surfaces files. I thought it'll be easier to create all of these files directly in RAS orientation.
Thanks, Noam -----Original Message----- From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Bruce Fischl Sent: Friday, March 8, 2019 11:05 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Cc: Sophie Esterer <ester...@cardiff.ac.uk> Subject: 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 > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
