Hi Haiyun
We reslice everything to coronal as part of the recon process. If you want to
map it back to the original orientation I think something like this should work:
mri_convert -rt nearest -rl rawavg.mgz aseg.mgz aseg.original_orientation.mgz
cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Haiyun Chen
Sent: Thursday, November 10, 2022 4:58 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] How to set original orientation for converted images
External Email - Use Caution
Hello FreeSurfer Experts,
I converted the aseg.mgz file to aseg.nii using mri_convert command,
the aseg.mgz file is located in the directory below based on your tutorial:
tutorial_data_20190918_1558/practice_with_data/Subj001/mri
When I open the file aseg.nii in a different application,
the original orientation is not sagittal.
In the MRI protocol, the original orientation is sagittal.
Could you please help to tell how to set the original orientation
of output images to be sagittal?
Thank you in advance!
Best regards
Haiyun
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