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| = THIS PAGE HAS BEEN MOVED TO SHAREPOINT! = Please refer to this site/make edits here for the most updated information: https://partnershealthcare.sharepoint.com/sites/LCN/SitePages/Longitudinal-Testing.aspx ---- <<BR>> <<BR>> <<BR>> |
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| ||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.|| || || | ||control points ||affected base surf; <<BR>>afffected long surfs ||affected long surfs ||affected long surfaces. || || || |
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| ||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. || | ||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 ||when edited this volume in cross, it was copied as brain.finalsurfs.manedit.mgz into the cross mri directory. Then, cross was submitted for rebuilding from the point of this edit using the flag -autorecon3-pial. The edits made in the cross transferred to the long. ||when edited brain.finalsurfs in base, it was copied as brain.finalsurfs.manedit.mgz into the base mri directory. Only then did these edits get incorporated into base upon re-building the base 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. || | ||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. || |
THIS PAGE HAS BEEN MOVED TO SHAREPOINT!
Please refer to this site/make edits here for the most updated information: 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. |
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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. |
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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. |
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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. |
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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. |
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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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