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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@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

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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