External Email - Use Caution
Hello FreeSurfers, We use a custom surface template, generated according to the instructions in the SurfaceRegAndTemplates https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates instructions for inter-subject co-registration. We then do cortical labeling and extract surface and volume stats. In the past, I would re-run mris_register, then jump to labeling using the resulting ?h.sphere.reg (using either a custom atlas or the labeled template surface), and then extract stats. However, I now see that there are steps in -autorecon3 stage of the recon-all workflow, including the pial surface generation step, that are done after the -surfreg step, but prior to stat extraction, that depend on ?h.sphere.reg. So it seems like I should be running the essentially the entire -autorecon3 stage (minus -sphere and the default surface labeling and stat extraction steps) with the custom surface template as input. Is that the case? If so, is there an "expert flag" to run these steps of -autorecon3 with a custom surface template (analogous to the -custom-tal-atlas flag for early stages?)
Thanks, Jason