Hello FreeSurfer expert,
I have a binarized stroke masks of 200 stroke patients that were hand traced. Since, we have a lot of patients, it will take a lot of time to edit the aseg.presurf.mgz. The stroke masks were drawn in the native space and I want to bring them into the freesurfer space, and combine with the aseg.presurf.mgz/stamp it onto the aseg.presurf.mgz and then run recon-all -autorecon2-noaseg -autorecon3.
I have done the first part: 1) mri_convert -rl /subject/mri/brainmask.mgz -rt nearest stroke.nii stroke.mgz (use freeview to check the accuracy)
I want to combine the stroke.mgz with the aseg.presurf.mgz in order to create a new ROI. what command should I use to accomplish this? Thanks
Best,
Paul
try something like
mergeseg --src aseg.presurf.mgz --merge stroke.mgz --o aseg.manedit.mgz --segid 77
This will model the strokes as WM hypointensities
On 09/07/2017 11:54 AM, miracle ozzoude wrote:
Hello FreeSurfer expert,
I have a binarized stroke masks of 200 stroke patients that were hand traced. Since, we have a lot of patients, it will take a lot of time to edit the aseg.presurf.mgz. The stroke masks were drawn in the native space and I want to bring them into the freesurfer space, and combine with the aseg.presurf.mgz/stamp it onto the aseg.presurf.mgz and then run recon-all -autorecon2-noaseg -autorecon3.
I have done the first part:
- mri_convert -rl /subject/mri/brainmask.mgz -rt nearest stroke.nii
stroke.mgz (use freeview to check the accuracy)
I want to combine the stroke.mgz with the aseg.presurf.mgz in order to create a new ROI. what command should I use to accomplish this? Thanks
Best,
Paul
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks doug. If I run the recon-all -autorecon2-noaseg -autorecon3. Will it incorporate the stroke? Also, does it matter if it's a cortical stroke and i am using v6.0 and i don't see aseg.manedit.mgz.
Best, Paul
On Thu, Sep 7, 2017 at 12:38 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
try something like
mergeseg --src aseg.presurf.mgz --merge stroke.mgz --o aseg.manedit.mgz --segid 77
This will model the strokes as WM hypointensities
On 09/07/2017 11:54 AM, miracle ozzoude wrote:
Hello FreeSurfer expert,
I have a binarized stroke masks of 200 stroke patients that were hand traced. Since, we have a lot of patients, it will take a lot of time to edit the aseg.presurf.mgz. The stroke masks were drawn in the native space and I want to bring them into the freesurfer space, and combine with the aseg.presurf.mgz/stamp it onto the aseg.presurf.mgz and then run recon-all -autorecon2-noaseg -autorecon3.
I have done the first part:
- mri_convert -rl /subject/mri/brainmask.mgz -rt nearest stroke.nii
stroke.mgz (use freeview to check the accuracy)
I want to combine the stroke.mgz with the aseg.presurf.mgz in order to create a new ROI. what command should I use to accomplish this? Thanks
Best,
Paul
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
sorry, should be
mergeseg --src aseg.auto.mgz --merge stroke.mgz --o aseg.presurf.mgz --segid 77
when you re-run recon-all, it will create the manedit file
On 09/07/2017 12:49 PM, miracle ozzoude wrote:
Thanks doug. If I run the recon-all -autorecon2-noaseg -autorecon3. Will it incorporate the stroke? Also, does it matter if it's a cortical stroke and i am using v6.0 and i don't see aseg.manedit.mgz.
Best, Paul
On Thu, Sep 7, 2017 at 12:38 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
try something like mergeseg --src aseg.presurf.mgz --merge stroke.mgz --o aseg.manedit.mgz --segid 77 This will model the strokes as WM hypointensities On 09/07/2017 11:54 AM, miracle ozzoude wrote: > Hello FreeSurfer expert, > > I have a binarized stroke masks of 200 stroke patients that were hand > traced. Since, we have a lot of patients, it will take a lot of time > to edit the aseg.presurf.mgz. The stroke masks were drawn in the > native space and I want to bring them into the freesurfer space, and > combine with the aseg.presurf.mgz/stamp it onto the aseg.presurf.mgz > and then run recon-all -autorecon2-noaseg -autorecon3. > > I have done the first part: > 1) mri_convert -rl /subject/mri/brainmask.mgz -rt nearest stroke.nii > stroke.mgz (use freeview to check the accuracy) > > I want to combine the stroke.mgz with the aseg.presurf.mgz in order to > create a new ROI. what command should I use to accomplish this? Thanks > > Best, > > Paul > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
miracle ozzoude