I was afraid of that. You will need to either map wmparc to the brainstem space or the brainstem into the wmparc. Probably better to do the first. You can use mri_label2vol with --seg wmparc.mgz --temp brainstem.mgz --regheader wmparc.mgz --o wmparc.in-brainstem.mgz
On 01/10/2018 11:54 AM, John Anderson wrote: > Dear Dr Greeve, > Thank you very much for the quick and detailed response. > Before your response, I tried fslmaths instead of fslcalc and I got > error message complains about misorientation between the input masks. > > Now, I tried fslcalc and it failed as well to combine the masks due to > a mismatch sizes! > Any suggestions are highly appreciated? > > > 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 > >> -------- Original Message -------- >> Subject: combining masks >> Local Time: January 10, 2018 11:10 AM >> UTC Time: January 10, 2018 4:10 PM >> From: john.ande...@protonmail.com >> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> >> 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.
