Dear FreeSurfer list,
I am making some manual correction to subcortical structures using Edit Segmentation Tool. And my question is: how should I proceed after saving aseg.mgz? Should I re-run autorecon2 with some options?
Thank you, Tanja.
You can just rerun autorecon2 and autorecon3. If you save it as aseg.mgz, it will recognize edits were made when you rerun.
On Mar 30, 2011, at 7:51 AM, Tetiana Dadakova tetiana.d@gmail.com wrote:
Dear FreeSurfer list,
I am making some manual correction to subcortical structures using Edit Segmentation Tool. And my question is: how should I proceed after saving aseg.mgz? Should I re-run autorecon2 with some options?
Thank you, Tanja. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Tanja unless the editing would change the cortex, you don't need to worry about it
Bruce On Wed, 30 Mar 2011, Tetiana Dadakova wrote:
Dear FreeSurfer list,
I am making some manual correction to subcortical structures using Edit Segmentation Tool. And my question is: how should I proceed after saving aseg.mgz? Should I re-run autorecon2 with some options?
Thank you, Tanja. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Bruce,
For some of my subjects the segmentation of putamen "sticks" to the cortex (please look at attached image "before.jpg"). Therefore, I do some manual corrections that affect the cortex (please look at attached image "after.jpg").
How should I proceed after this kind of manual correction?
Thank you, Tanja.
On Wed, Mar 30, 2011 at 3:31 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Tanja unless the editing would change the cortex, you don't need to worry about it
Bruce On Wed, 30 Mar 2011, Tetiana Dadakova wrote:
Dear FreeSurfer list,
I am making some manual correction to subcortical structures using Edit Segmentation Tool. And my question is: how should I proceed after saving aseg.mgz? Should I re-run autorecon2 with some options?
Thank you, Tanja. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Tanja
yes, there is really no visible extreme capsule white matter, I guess because it is so thin. If you are trying to fix the surfaces you will want to edit the wm.mgz though, not the aseg.mgz.
cheers Bruce
On Thu, 5 May 2011, Tetiana Dadakova wrote:
Dear Bruce,
For some of my subjects the segmentation of putamen "sticks" to the cortex (please look at attached image "before.jpg"). Therefore, I do some manual corrections that affect the cortex (please look at attached image "after.jpg").
How should I proceed after this kind of manual correction?
Thank you, Tanja.
On Wed, Mar 30, 2011 at 3:31 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Tanja unless the editing would change the cortex, you don't need to worry about it
Bruce On Wed, 30 Mar 2011, Tetiana Dadakova wrote:
Dear FreeSurfer list,
I am making some manual correction to subcortical structures using Edit Segmentation Tool. And my question is: how should I proceed after saving aseg.mgz? Should I re-run autorecon2 with some options?
Thank you, Tanja. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Thank you Bruce,
So if I want to edit both cortex and subcortical structures, should the steps be the following:
1. edit wm.mgz 2. recon-all -autorecon2-wm -subjid 3. edit subcortical structures 4. recon-all -autorecon2 -autorecon3 -subjid ?
Best wishes, Tanja.
On Thu, May 5, 2011 at 2:40 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Tanja
yes, there is really no visible extreme capsule white matter, I guess because it is so thin. If you are trying to fix the surfaces you will want to edit the wm.mgz though, not the aseg.mgz.
cheers Bruce
On Thu, 5 May 2011, Tetiana Dadakova wrote:
Dear Bruce,
For some of my subjects the segmentation of putamen "sticks" to the cortex (please look at attached image "before.jpg"). Therefore, I do some manual corrections that affect the cortex (please look at attached image "after.jpg").
How should I proceed after this kind of manual correction?
Thank you, Tanja.
On Wed, Mar 30, 2011 at 3:31 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Tanja unless the editing would change the cortex, you don't need to worry about it
Bruce On Wed, 30 Mar 2011, Tetiana Dadakova wrote:
Dear FreeSurfer list,
I am making some manual correction to subcortical structures using Edit Segmentation Tool. And my question is: how should I proceed after saving aseg.mgz? Should I re-run autorecon2 with some options?
Thank you, Tanja. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
or edit them both and run
recon-all -autorecon2 -autorecon3 -subjid ?
I think should work On Thu, 5 May 2011, Tetiana Dadakova wrote:
Thank you Bruce,
So if I want to edit both cortex and subcortical structures, should the steps be the following:
- edit wm.mgz
- recon-all -autorecon2-wm -subjid
- edit subcortical structures
- recon-all -autorecon2 -autorecon3 -subjid ?
Best wishes, Tanja.
On Thu, May 5, 2011 at 2:40 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Tanja
yes, there is really no visible extreme capsule white matter, I guess because it is so thin. If you are trying to fix the surfaces you will want to edit the wm.mgz though, not the aseg.mgz.
cheers Bruce
On Thu, 5 May 2011, Tetiana Dadakova wrote:
Dear Bruce,
For some of my subjects the segmentation of putamen "sticks" to the cortex (please look at attached image "before.jpg"). Therefore, I do some manual corrections that affect the cortex (please look at attached image "after.jpg").
How should I proceed after this kind of manual correction?
Thank you, Tanja.
On Wed, Mar 30, 2011 at 3:31 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Tanja unless the editing would change the cortex, you don't need to worry about it
Bruce On Wed, 30 Mar 2011, Tetiana Dadakova wrote:
Dear FreeSurfer list,
I am making some manual correction to subcortical structures using Edit Segmentation Tool. And my question is: how should I proceed after saving aseg.mgz? Should I re-run autorecon2 with some options?
Thank you, Tanja. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
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Allison Stevens -
Bruce Fischl -
Tetiana Dadakova