Freesurfer lh.pial and rh.pial xyz coordinates are reported in tkregister space.

I believe you need to convert tkrRAS to RAS space using vox2ras * inv(vox2ras-tkr). ‘vox2ras’ and ‘vox2ras-tkr’ matrix are reported in mris_info.

If you are using Freesurfer dev version, these three TAGs (TAG_SURF_DATASPACE, TAG_SURF_MATRIXDATA, TAG_SURF_TRANSFORMEDSPACE) are available in the surface files. You can use TAG_SURF_MATRIXDATA to convert [x, y, z] coordinates between TAG_SURF_DATASPACE and TAG_SURF_TRANSFORMEDSPACE.

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of ???
Sent: Monday, July 15, 2024 5:05 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] (no subject)

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Dear Freesurfer Team

    I have extracted the left and right cerebral cortex from the aseg.mgz file in the 3d slicer. 

    At the same time, I have loaded the lh.pial and rh.pial in the 3d slicer

    the left and right cerebral cortex extracted from the aseg.mgz file was not in the same position with the lh.pial and rh.pial in the 3d slicer

    How should I put them in the same position in the 3d slicer

Thanks 

Mengjun