I am looking for a way to extract thickness values at the level of each vertex from Freesurfer atlas-based parcellated regions (aparc.annot), or more generally lobes. Is this possible? 

Using mri_segstats I know it is possible to get more general metrics such as min, max and average thickness values, and # of voxels. Is it possible to use an annot file to read out the raw thickness values? 

This post was the closest I could find to answering my question, however, this was at the group level and not specified for parcellated regions. https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022097.html

Thank you in advance,

Lindsay

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