| Deletions are marked like this. | Additions are marked like this. |
| Line 2: | Line 2: |
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||Edit Type ||cross ||base ||long ||flag ||additional scenarios || ||control points ||X || || || || || ||brainmask || ||X|| || || || ||wm ||X || || || || || ||aseg ||X|| || || || || ||brainfinalsurfs || || || || || || ||seed point, watershed ||X|| || || || || ||cw256 ||X|| || || || || ||talairach || || || || || || ||xopts || || || || || || ||seed point, fill & cut || || || || || || |
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| Line 3: | Line 14: |
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|| 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 || || || || || || |
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| Line 16: | Line 16: |
| * After editing the base, must run both -autorecon2 & -autorecon3 for longitudinal runs to run successfully. | * After editing the base (only wm.mgz edits), must run both -autorecon2 & -autorecon3 for longitudinal runs to run successfully. |
| Line 18: | Line 18: |
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|| 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 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|| || || ||talairach || || || || || || ||xopts || || || || || || ||seed point, fill & cut || || || || || || |
Done
Edit Type |
cross |
base |
long |
flag |
additional scenarios |
control points |
X |
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brainmask |
|
X |
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wm |
X |
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aseg |
X |
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brainfinalsurfs |
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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 (only wm.mgz 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 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 |
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|
brainfinalsurfs |
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seed point, watershed |
can only adjust wsthresh for cross; edits copied to base |
n/a |
n/a |
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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 |
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seed point, fill & cut |
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