Dear Freesurfer experts, I would like to get a map of scalp-cortex distance for every vertex on the pial surface (for use in predicting the effects of TMS). I believe there is no existing automated method for doing this.
Are there any suggestions for how to calculate a scalp-cortex distance map? My current plan is simply rename my files so that the outer_skin takes the place of the pial surface, and the pial surface takes the place of the white matter boundary. Would this allow me to run mri_thickness as normal and get a scalp-cortex distance map? Alternatively, I might create a new version of mris_thickness.c in which all references to the "white" surface are replaced with references to the outer_skin surface constructed by mri_watershed, though I am new to c and thus hesitant to take this approach. (Also, I have only a MEMPRAGE and no FLASH 5/30 sequences, so I cannot use mri_make_bem_surfaces; is the latter is still considered preferable?) Any suggestions or thoughts would be highly appreciated.
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