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Size: 1386
Comment:
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Size: 2779
Comment:
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| Deletions are marked like this. | Additions are marked like this. |
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| ||control points ||X || || || || || ||brainmask || ||X|| || || || ||wm ||X || || || || || ||aseg ||X|| || || || || ||brainfinalsurfs || || || || || || ||seed point, watershed ||X|| || || || || ||cw256 ||X|| || || || || |
||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 || || || || || |
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| * After editing the base (only wm.mgz edits), 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 20: | Line 20: |
| ||control points ||affected base surfs || || || || || ||brainmask || ||affected long surfs|| || || || ||wm ||edits copied to long when long run from scratch; surfs for base and long unchanged ||affected long surfs|| || ||test edits in cross w/o removing long || ||aseg ||edits copied to long but changes are unpredictable|| || || || || ||brainfinalsurfs || || || || || || ||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|| || || |
||control points ||affected base surf; <<BR>>afffected long surfs ||affected long surfs ||control points added to brainmask function as expected - need to check intensity of reconstructed brainmask.|| || || ||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 ||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. || ||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, and run "recon-all -autorecon3-pial -long" on the subject. The edits do take effect and the pial surface is pulled in as desired. || ||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 || || || |
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Done
Edit Type |
cross |
base |
long |
flag |
additional scenarios |
control points |
X |
X |
X |
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|
brainmask |
X |
X |
X |
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|
wm |
X |
X |
X |
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|
aseg |
X |
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|
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 |
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|
cw256 |
X |
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|
talairach |
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xopts |
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seed point, fill & cut |
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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; |
affected long surfs |
control points added to brainmask function as expected - need to check intensity of reconstructed brainmask. |
|
|
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 |
edits copied to long when long run from scratch; |
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. |
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, and run "recon-all -autorecon3-pial -long" on the subject. The edits do take effect and the pial surface is pulled in as desired. |
|
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; |
n/a |
n/a |
|
|
cw256 |
only have to use this flag once w/ recon-all for cross |
n/a |
n/a |
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|
talairach |
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|
|
xopts |
|
|
|
|
|
seed point, fill & cut |
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