= Done =
||Edit Type ||cross ||base ||long ||flag ||additional scenarios ||
||control points ||X ||X ||X || || ||
||brainmask ||X ||X ||X || || ||
||wm ||X ||X ||X || || ||
||aseg ||X || || || || ||
||brainfinalsurfs ||X ||X ||X || ||Edits made to both cross and base transfer to long; remember to create brain.finalsurfs.manedit.mgz files.Surfaces in long initiated from base but take final destination cues from cross.||
||seed point, watershed ||X || || || || ||
||cw256 ||X || || || || ||
||talairach || || || || || ||
||xopts || || || || || ||
||seed point, fill & cut || || || || || ||


== Notes ==
* After editing the base (for wm.mgz and CPs edits), must run both -autorecon2 & -autorecon3 for longitudinal runs to run successfully.

* After editing the cross-sectionals, it is ok to just run -autorecon2 without -autorecon3.
||Edit Type ||cross ||base ||long ||flag ||additional scenarios ||
||control points ||affected base surf; <<BR>>afffected long surfs ||affected long surfs ||affected long surfaces. || || ||
||brainmask ||need to delete base and rerun from scratch in order for edits to work ||affected long surfs ||both small and large scale brainmask edits are incorporated as expected. || || ||
||wm added ||edits copied to long when long run from scratch; <<BR>>surfs for base and long unchanged ||affected long surfs ||edit wm volume, re-run w/ -autorecon2-wm; Result is corrections to wm volume without corresponding change in white surface. || ||white surface in long is initiated from base, and will only grow outward following wm volume in cross. Will not pull in even if cross wm volume is severely truncated. ||
||wm removed ||     ||      || edit wm volume, re-run w/ -autorecon2-wm; Result is corrections to wm volume without corresponding change in white surface. || ||white surface in long is initiated from base, and will only grow outward following wm volume in cross. Will not pull in even if cross wm volume is severely truncated. ||
||aseg ||edits copied to long but changes are unpredictable || || || || ||
||brainfinalsurfs ||Remember to copy edited brain.finalsurfs volume to brain.finalsurfs.manedit.mgz , if only this volume edited, re-run using -autorecon3-pial.|| Remember to copy edited brain.finalsurfs volume to brain.finalsurfs.manedit.mgz , if only this volume edited, re-run using -autorecon3-pial.||Edit the brain.finalsurfs.mgz volume, make a copy of this edited volume to brain.finalsurfs.manedit.mgz;if only this volume edited, re-run using -autorecon3-pial.  || ||Edits must be made in cross and base in order to edit the longitudinal whose errors stem from the cross and base. ||
||seed point, watershed ||can only adjust wsthresh for cross; <<BR>>edits copied to base ||n/a ||n/a || || ||
||cw256 ||only have to use this flag once w/ recon-all for cross ||n/a ||n/a || || ||
||talairach || || || || || ||
||xopts || || || || || ||
||seed point, fill & cut || || || || || ||


For LCN faculty and staff, this information is also documented here: https://partnershealthcare.sharepoint.com/sites/LCN/SitePages/Longitudinal-Testing.aspx