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.
