The actual orientation of the input should not matter as long as the nominal orientation matches the true orientation -- FS automatically handles the orientation correctly. When you ask whether the output will be "in RAS", are you asking whether the left side is truly the left (and right is right)? If so, the answer is yes.
On 5/4/2020 12:50 PM, Peled, Noam wrote:
Hello,
After running recon-all on a patient, the resulting T1.mgz coordinates system turned to be LIA. Can I guarantee the recon-all output will be in RAS?
I also would like to run FS-FAST on this patient’s fMRI task dataset, which is in LSA.
Any recommendation what should I do to make sure both are in the same coordinates system (I preferred RAS)?
Thanks,
Noam
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