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 <gr...@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 > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@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. > >
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