Differences between revisions 1 and 28 (spanning 27 versions)

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; 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

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

-  ⇤ ← Revision 1 as of 2011-03-08 19:04:42 → 
  Size: 1200
  Editor: AllisonStevens
  Comment:
+   ← Revision 28 as of 2021-05-03 08:12:06 → ⇥
  Size: 3125
  Editor: DevaniCordero
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 1:
-Line 2:
+Line 3:
+||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 || || || || || ||
-Line 3:
+Line 15:
-|| Edit Type || cross || base || long || flag || additional scenarios ||
|| control points || X ||  ||  ||  ||  ||
|| brainmask ||  ||  ||  ||  ||  ||
|| wm || X ||  ||  ||  ||  ||
|| aseg ||  ||  ||  ||  ||  ||
|| brainfinalsurfs ||  ||  ||  ||  ||  ||
|| seed point, watershed ||  ||  ||  ||  ||  ||
|| cw256 ||  ||  ||  ||  ||  ||
|| talairach ||  ||  ||  ||  ||  ||
|| xopts ||  ||  ||  ||  ||  ||
|| seed point, fill & cut ||  ||  ||  ||  ||  ||
-Line 16:
+Line 17:
-* After editing the base, must run both -autorecon2 & -autorecon3 for longitudinal runs to run successfully.
+* After editing the base (for wm.mgz and CPs edits), must run both -autorecon2 & -autorecon3 for longitudinal runs to run successfully.
-Line 18:
+Line 19:
-|| Edit Type || cross || base || long || flag || additional scenarios ||
|| control points || affected base surfs ||  ||  ||  ||  ||
|| brainmask ||  ||  ||  ||  ||  ||
|| wm || edits copied to long when long run from scratch || surfaces unchanged || surfaces unchanged ||  || test edits in cross w/o removing long ||
|| aseg ||  ||  ||  ||  ||  ||
|| brainfinalsurfs ||  ||  ||  ||  ||  ||
|| seed point, watershed ||  ||  ||  ||  ||  ||
|| cw256 ||  ||  ||  ||  ||  ||
|| talairach ||  ||  ||  ||  ||  ||
|| xopts ||  ||  ||  ||  ||  ||
|| seed point, fill & cut ||  ||  ||  ||  ||  ||
+* 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