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:* freesurfer-bounces@nmr.mgh.harvard.edu > <freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Douglas N. > Greve *Sent:* Monday, August 17, 2020 10:24 AM *To:* > freesurfer@nmr.mgh.harvard.edu *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 > > > > > > > > > > > > > > > > > > ------------------------- > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If > you are not the intended recipient, be advised that any unauthorized > use, disclosure, copying or the taking of any action in reliance on > the contents of this information is strictly prohibited. If you have > received this email in error, please immediately notify the sender > via telephone or return mail. > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > ------------------------- > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If > you are not the intended recipient, be advised that any unauthorized > use, disclosure, copying or the taking of any action in reliance on > the contents of this information is strictly prohibited. If you have > received this email in error, please immediately notify the sender > via telephone or return mail. > > > _______________________________________________ Freesurfer mailing > list Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer