When working with area, you need to turn on jacobian correction. mris_preproc will do this automatically, but you have to add --jac to mri_surf2surf explicitly

On 3/20/2024 4:31 AM, tyzhang@ibp.ac.cn wrote:

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Dear FreeSurfer Experts,

I'm currently working on mapping cortical morphometric measurements from each individual in the HCP dataset to the fsaverage space.

I have noticed that both the mris_preproc and mri_surf2surf commands can achieve this function. However, I found that the vertex-level measurements for cortical thickness, sulcal depth, and curvatures are consistent between these two commands, but the results for surface area and gray matter volume are totally different.

I am puzzled by this inconsistency and speculate that perhaps these two commands are calculated on different surfaces? I don't understand why the two commands get different results since the inputs are the same.

My command are as follows: (Different surface area values will be obtained in lh.area.fsaverage.mgh and lh.area.fsaverage.gii files)

mris_preproc --s  id  --meas  area --target fsaverage --hemi lh –out /Results/CorticalFeatures/id/lh.area.fsaverage.mgh

mri_surf2surf --srcsubject id --trgsubject fsaverage --hemi lh --sval /HCP/id/surf/lh.area --tval /Results/CorticalFeatures/id/lh.area.fsaverage.gii

Thank you so much!

Tongyu Zhang

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