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Size: 1386
Comment:
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Size: 2154
Comment:
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| Deletions are marked like this. | Additions are marked like this. |
| Line 3: | Line 3: |
| ||control points ||X || || || || || ||brainmask || ||X|| || || || ||wm ||X || || || || || ||aseg ||X|| || || || || ||brainfinalsurfs || || || || || || ||seed point, watershed ||X|| || || || || ||cw256 ||X|| || || || || |
||control points ||X ||X || || || || ||brainmask ||X ||X || || || || ||wm ||X ||X || || || || ||aseg ||X || || || || || ||brainfinalsurfs ||X||X|| || ||Editing both cross and base was done, and effect on long was observed Results of edits are as follows: Edits to the brain.finalsurfs volume to fix the pial surface around the cerebellum are transferred from both base and cross to the corresponding long. Surfaces are initiated from the base but volume and surface final appearance features are dictated by the cross. Thus, one must edit the cross (one, or both, if both crosses have errors to this volume) and then recreate a new base, and then create new long files. One will see the edits incoporated into the long to produce a more accurate pial surface as desired. || ||seed point, watershed ||X || || || || || ||cw256 ||X || || || || || |
| Line 16: | Line 16: |
| * 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|| || || || || |
||control points ||affected base surf; <<BR>>afffected long surfs ||affected long surfs || || || || ||brainmask ||need to delete base and rerun from scratch in order for edits to work ||affected long surfs || || || || ||wm ||edits copied to long when long run from scratch; <<BR>>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 || || || || || |
| Line 25: | Line 25: |
| ||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|| || || |
||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 || || || |
Done
Edit Type |
cross |
base |
long |
flag |
additional scenarios |
control points |
X |
X |
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brainmask |
X |
X |
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|
wm |
X |
X |
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aseg |
X |
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|
brainfinalsurfs |
X |
X |
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|
Editing both cross and base was done, and effect on long was observed Results of edits are as follows: Edits to the brain.finalsurfs volume to fix the pial surface around the cerebellum are transferred from both base and cross to the corresponding long. Surfaces are initiated from the base but volume and surface final appearance features are dictated by the cross. Thus, one must edit the cross (one, or both, if both crosses have errors to this volume) and then recreate a new base, and then create new long files. One will see the edits incoporated into the long to produce a more accurate pial surface as desired. |
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 |
|
|
|
brainmask |
need to delete base and rerun from scratch in order for edits to work |
affected long surfs |
|
|
|
wm |
edits copied to long when long run from scratch; |
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; |
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 |
|
|
|
|
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