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Size: 1488
Comment:
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Size: 2779
Comment:
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| Deletions are marked like this. | Additions are marked like this. |
| Line 3: | Line 3: |
| ||control points ||X || || || || || ||brainmask ||X||X || || || || ||wm ||X || || || || || |
||control points ||X ||X ||X || || || ||brainmask ||X ||X ||X || || || ||wm ||X ||X ||X || || || |
| Line 7: | Line 7: |
| ||brainfinalsurfs || || || || || || | ||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.|| |
| Line 20: | Line 20: |
| ||control points ||affected base surfs || || || || || ||brainmask ||did not affect the base and therefore did not affect the long ||affected long surfs || || ||*retesting*|| ||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 || |
||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. || |
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| ||brainfinalsurfs || || || || || || | ||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. || |
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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 |
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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 |
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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 |
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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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