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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 [cid:image001.jpg@01D6718F.CD2B0920]
[cid:image002.jpg@01D6718F.CD2B0920]
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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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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 [cid:image001.jpg@01D6748C.ABF39880]
[cid:image002.jpg@01D6748C.ABF39880]
________________________________ 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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________________________________ 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.
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
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Thx Doug. I'll give it a shot.
Get Outlook for Androidhttps://aka.ms/ghei36 ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu > freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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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