The --in_orientation should work. The RAS coordinates will reflect subject space (which is probably what you want) and not scanner space.
On 5/7/2019 11:27 AM, Caspar M. Schwiedrzik wrote:
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Hi! I have data acquired on a Siemens scanner with head first-prone. When I convert the dicom files to MGZ, left and right and superior and inferior, respectively, are swapped. The anterior-posterior dimension is ok. I am wondering what the correct way to correct this is?
Following this entry in the wiki https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal, it seems that I can use mri_convert with --in_orientation for that, and the images indeed look correct when I do this. I am however wondering whether I have to do the conversion to COR and fix the RAS coordinates as well? I found a 2007 entry on the mailing list about that https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2007-October/006250.ht..., but it does not specify how to proceed.
Your advice would be appreciated! Thanks, Caspar
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