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Size: 2154
Comment:
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← Revision 28 as of 2021-05-03 08:12:06 ⇥
Size: 3125
Comment:
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| Deletions are marked like this. | Additions are marked like this. |
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| ||control points ||X ||X || || || || ||brainmask ||X ||X || || || || ||wm ||X ||X || || || || |
||control points ||X ||X ||X || || || ||brainmask ||X ||X ||X || || || ||wm ||X ||X ||X || || || |
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| ||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. || | ||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.|| |
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| ||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 || |
||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. || |
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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;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. || |
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| For LCN faculty and staff, this information is also documented here: https://partnershealthcare.sharepoint.com/sites/LCN/SitePages/Longitudinal-Testing.aspx |
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 |
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; |
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 |
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|
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;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; |
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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For LCN faculty and staff, this information is also documented here: https://partnershealthcare.sharepoint.com/sites/LCN/SitePages/Longitudinal-Testing.aspx