Done

Edit Type

cross

base

long

flag

additional scenarios

control points

X

X

X

brainmask

X

X

X

wm

X

X

X

aseg

X

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.

seed point, watershed

X

cw256

X

talairach

xopts

seed point, fill & cut

Edit Type

cross

base

long

flag

additional scenarios

control points

affected base surf;
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 to remove non-brain voxels for purpose of pulling pial surface in, are successfully incoporated to correct the pial surface as desired.

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;
surfs for base and long unchanged

affected long surfs

When wm voxels are removed or added to the wm volume, and -autorecon2-wm is run, the result is the disappearance or appearance, respectively, of the edited voxels but no corresponding change of the white surface - that is, surface does not pull in or grow with changes to wm volume. Surfaces are initialized from the base and do not shrink or grow to fit the wm volume in the cross/long.

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

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.

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

talairach

xopts

seed point, fill & cut