you can try something like
mri_convert aseg.mgz --out_orientation PIL aseg.sag.nii.gz

On 11/18/2022 4:31 PM, Haiyun Chen wrote:

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Hello Freesurfer Experts,

How can we set the original orientation of an image file such that when the image is opened in a different application   the original orientation is a sagittal viewport?

For the file aseg.mgz in the below directory based on your tutorial, could you please tell a specific command to convert aseg.mgz to a file with sagittal viewport as the original orientation?

tutorial_data_20190918_1558/practice_with_data/Subj001/mri/aseg.mgz

Thank you in advance!

Best regards

Haiyun

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