External Email - Use Caution Thx Doug. I'll give it a shot.
Get Outlook for Android<https://aka.ms/ghei36> ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgr...@mgh.harvard.edu> Sent: Monday, August 17, 2020 12:31:58 PM To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FS edits of subcortical parcels * External Email - Caution * 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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > > > > > <freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > > *On Behalf Of *Douglas N. > Greve *Sent:* Monday, August 17, 2020 10:24 AM > > *To:* > > > freesurfer@nmr.mgh.harvard.edu<mailto: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> > > > <mailto: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<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.
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