Start with editing aseg.manedit.mgz; these changes will propagate into
wm.mgz, so only edit wm.mgz if it is wrong after the edits. Replace the
voxels labels with the correct ones. In V6 run
recon-all -s subject -autorecon2 -nogcareg -nocanorm -nocareg -autorecon3
I would suggest doing a test on one subject to make sure that the edits
get propagated properly. This is not the kind of thing we do that often,
so use caution.
On 8/17/2020 12:59 PM, Alexopoulos, Dimitrios wrote:
> External Email - Use Caution > > Thx Doug. I presume I can just make
WM edits to the wm.mgz at > periphery of the ventricle but how about
caudate/lentiform edits > (which I have never had to do) . Do I replace
incorrect voxels with > the correct aseg labels (i.e. R caudate label
50) with the aseg being > the Reference volume? > > > > I’m using FS 6.0
Can I just run ‘recon-all –all’ again after all the > edits? > > > > Jim
> > > > *From:* [email protected] >
<[email protected]> *On Behalf Of *Douglas N. >
Greve *Sent:* Monday, August 17, 2020 10:24 AM *To:* >
[email protected] *Subject:* Re: [Freesurfer] FS edits > of
subcortical parcels > > > > ** External Email - Caution ** > > Copy
aseg.auto.mgz to aseg.manedit.mgz, then edit aseg.manedit.mgz. > If you
are using v7, then you can run recon-all -s subject > -autorecon2-samseg
-autorecon3 > > > On 8/13/2020 5:35 PM, Alexopoulos, Dimitrios wrote: >
> * External Email - Use Caution * > > FS editing experts, I have a
subject with enlarged ventricles and > processed the subject with
recon-all –bigventricles flag. > > > > The surfaces look good but the
subcortical segmentation and some WM > around the ventricles ,
especially for the right hem, are poor. > > Images below. What is the
best approach to edit this segmentation? > There are some WM edits
required and some caudate, lentiform edits > as well. Is the aseg or
aseg+aparc edited? > > > > Jim > > > > > > > > > > > > > > > > > >
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