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 MailScanner has detected a possible fraud attempt from "urldefense.proofpoint.com" claiming to be 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 MailScanner has detected a possible fraud attempt from "urldefense.proofpoint.com" claiming to be https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2007-October/006250.html, but it does not specify how to proceed.

Your advice would be appreciated!

Thanks, Caspar

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