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| ||brainmask ||need to delete base and rerun from scratch in order for edits to work ||affected long surfs || || || || | ||brainmask ||need to delete base and rerun from scratch in order for edits to work ||affected long surfs || || ||pial surface was edited in both cross sectional tp's by editing brainmask : removal of areas of dura from brainmask. It was found that these edits DO transfer successfully to the base upon reconstruction of base from both crosses, and further, these edits DO transfer to long, which is constructed from both the edited crosses and the base created from edited crosses. || |
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. However, the edited brain.finalsurfs volumes in tkmedit for the cross and base must be copied as a brain.finalsurfs.manedit.mgz files into the respective cross and base directories before submitting for recreation of the long. 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 |
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brainmask |
need to delete base and rerun from scratch in order for edits to work |
affected long surfs |
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pial surface was edited in both cross sectional tp's by editing brainmask : removal of areas of dura from brainmask. It was found that these edits DO transfer successfully to the base upon reconstruction of base from both crosses, and further, these edits DO transfer to long, which is constructed from both the edited crosses and the base created from edited crosses. |
wm |
edits copied to long when long run from scratch; |
affected long surfs |
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test edits in cross w/o removing long When edits are made in cross and a new base is constructed from cross, base is not affected in wm volume or white surfaces because these are created in the base after branching from the cross at norm.mgz. When new cross and base used to construct long, it is seen that the white surface is initiated from the base, and can only grow outward to follow the wm volume, which is taken from the cross. The white surface will not draw inward in the long even if the wm volume dictated by the cross is severely truncated in certain areas. |
aseg |
edits copied to long but changes are unpredictable |
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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. |
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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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