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Great, thanks a lot, Doug! Caspar
On Tue, May 7, 2019 at 17:46 Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu wrote:
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:
External Email - Use CautionHi! 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 https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_fswiki_LeftRightReversal&d=DwMGaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8&m=cI2TpE_SkFvbwqC84Bc86jo4ozmgNkmU13xjkDLys9A&s=EXeP167X4yKEzh0Lgc89nZnwFDSIYSl94unVCZxVDsQ&e=, 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... https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_pipermail_freesurfer_2007-2DOctober_006250.html&d=DwMGaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8&m=cI2TpE_SkFvbwqC84Bc86jo4ozmgNkmU13xjkDLys9A&s=onANhhGknqVlwbUsGqed52ahoM3izfYDJuN30UbXjC8&e=, but it does not specify how to proceed.
Your advice would be appreciated! Thanks, Caspar
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