Thanks Doug! Good to know that. I realized I had a problem when I got activation on the wrong side (right finger tapping shows activation on the right hemisphere) The analysis was done in another hospital when I just helped them remotely. They told me that their analysis software shows the activation is in the other hemisphere.
Any idea why something like that can happen? Thanks, Noam From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Douglas N. Greve Sent: Monday, May 4, 2020 1:03 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all and fMRI coordinates mismatch 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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