Dear FreeSurfer community,
I've been unable to get my recon-all commands to work, and this appears to be because my output orientations are wrong.
As input, I am using .nii.gz structural images (from 3 different scanners: a Siemens Sonata (1.5T), Siemens Trio (3T) GE Signa (1.5T))
Using FSLview, I've looked at the input structural images and I believe my input orientations are all fine and consistent across all the files. My output talairach.xfm, and orig.mgz, appear with the axial and coronal images "swapped" (one is labelled as the other) and my saggital images appear oddly too, with the nose down.
I believe you have had reports of this problem before but I have not found a solution in my case.
Thanks and my warm regards, Amy
Dr Amy Bilderbeck D.Phil Experimental Psychology Department of Psychiatry, University of Oxford