Based on our understanding of the longitudinal pipeline for 4.5, image edits for the -long runs come mostly from the template/base subj (with an optional flag for CPs to be copied from the template; http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg13256.html, http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12895.html). In addition, our assumption is that pial edits will come via the template, as the -long brainmask, is a result of masking the -long T1.mgz by the template brainmask.mgz (which itself is the norm_template.mgz, a combination of every time point's norm.mgz [which is pre-edit stage]).
We've run into an issue where our -long runs are still in need of pial editing, despite edits having been done to both the cross sectional and template runs (see attached). However, it's also our understanding that we should not edit the -long runs and try to re-run (using -autorecon2-pial -autorecon3), as this will pollute the correction for intrasubject variation (per communication from Martin). How would you recommend to proceed? Thanks.
-Derin