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
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