You are right except for the last step. The surfaces are not retessellated to a common space. When it comes time for group analysis, overlays (eg, thickness) are sampled into the group space (not the surfaces themselves)

On 9/24/2020 9:40 PM, Pam Garcia wrote:

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Thanks for your response Bruce, just to clarify

If I understood, the wm surface is created using a surface deformation procedure that adaptively determined the MR intensity of the boundaries in question at each point in the cortex. Next a sphere from the wm inflated surface is computed, warps the sphere into a 2-D file containing the curvature and convexity patterns of the subject, and then registers the 2D file with a reference (parameterization template). This is executed to ensure that the curvature and convexity patterns are aligned with a generic reference template. The mean and the variance of curvature and convexity from the smooth and inflated surface are used in order to do more robust the register. Finally, the pial surface is created by expanding the white matter surface so that it closely follows the gray-CSF intensity gradient, keeping the same topology (number of vertex, edges, faces) and the vertex index is preserved. Finally, the vertex of the wm and pial surface are mapped in a common space and is here where we obtained vertex correspondence across the subjects.

Thanks

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Hi Pam

Yes, that’s pretty accurate.

Cheers Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Pam Garcia Sent: Thursday, September 24, 2020 9:40 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] parameterization template and the vertex in the pial surface

External Email - Use Caution Thanks for your response Bruce, just to clarify

If I understood, the wm surface is created using a surface deformation procedure that adaptively determined the MR intensity of the boundaries in question at each point in the cortex. Next a sphere from the wm inflated surface is computed, warps the sphere into a 2-D file containing the curvature and convexity patterns of the subject, and then registers the 2D file with a reference (parameterization template). This is executed to ensure that the curvature and convexity patterns are aligned with a generic reference template. The mean and the variance of curvature and convexity from the smooth and inflated surface are used in order to do more robust the register. Finally, the pial surface is created by expanding the white matter surface so that it closely follows the gray-CSF intensity gradient, keeping the same topology (number of vertex, edges, faces) and the vertex index is preserved. Finally, the vertex of the wm and pial surface are mapped in a common space and is here where we obtained vertex correspondence across the subjects. Thanks