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Dear FreeSurfer team, I'm working on a project where I need to align an existing FreeSurfer segmentation (from an older T1 image) with a the same T1 image of the same subject, but it is debiased and in a different atlas space. The goal is to leverage the manual edits and refinements made in the original FreeSurfer output while utilizing the improved image quality of the new T1 scan. Current approach:

1. Using mri_robust_register to align the old FreeSurfer T1 to the new T1 image 2. Applying the resulting transformation to all FreeSurfer volumes (mri/*.mgz files) 3. Transforming the surface files using mri_surf2surf 4. Running recon-all -autorecon2-cp -autorecon3 on the transformed data

Main Issue: After applying our current approach, we've noticed that while the volume files (mri/.mgz) seem to align well with the new T1 image, the surface files (surf/.pial, surf/*.white, etc.) are not aligning properly. This misalignment is causing discrepancies in our cortical measurements and affecting downstream analyses. Questions:

1. Is our approach appropriate for maintaining the quality of the original segmentation while adapting to the new T1 image? 2. Why might the surface files be misaligned when the volume files seem to align correctly? 3. Are there alternative methods or additional steps we should consider to ensure proper alignment of both volume and surface files? 4. How can we ensure that manually edited regions in the original segmentation are preserved, especially for surface-based edits? 5. Are there specific quality control steps you'd recommend for verifying both volume and surface alignment?

Any guidance, alternative approaches, or explanations you could provide would be greatly appreciated.

Thanks, Maame

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