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

Edit Type

cross

base

long

flag

additional scenarios

control points

affected base surf;
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;
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;
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