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 > <gr...@nmr.mgh.harvard.edu <mailto: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 > <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 > gr...@nmr.mgh.harvard.edu <mailto:gr...@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 -- 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
