you'll need to do it in 3 steps mri_binarize --i wmparc.mgz --match 1024 2024 3024 4024 --o wmparc.mask.mgz
mri_binarize --i brainstemSsLabels.v10.mgz --match 173 --o bs.mask.mgz fscalc wmparc.mask.mgz and bs.mask.mgz -o final.mask.mgz The only problem will be if the brainstem seg is higher res than wmpar On 01/10/2018 11:10 AM, John Anderson wrote: > Dear Freesurfer experts, > I want to create mask for the midbrain and the precentral gyrus. > I used FSV6 to do the reconstruction. Then I used the flag > -brainstem-structures in recon-all to segment the brain stem. > How can I create _one mask_ that include structures from wmpac.mgz and > brainstemSsLabels.v10.mgz for instance > I want to use mri_binarize to create one mask contains the following > labels > 1024 2024 3024 4024 from wmpar.mgz and 173 from brainstemSsLabels.v10.mgz > > Any advice you provide is highly appreciated. > Thanks > John > > > > _______________________________________________ > 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.
