Sorry for the delay. First run mni152reg for each subject (should take only a few min, but needs FSL I think). Then run
mri_label2vol --aparc+aseg --temp MNI152_2mm.nii.gz --reg $SUBJECTS_DIR/subject/mri/transforms/reg.mni152.2mm.lta --o aparc+aseg.subject.mni152_2mm.nii.gz On 11/14/2017 06:32 PM, Daya P wrote: > Hi all, > > I am still struggling with my previous question > > I processed a bunch of subjects using recon-all, but now I would like > to get labels from aparc.a2009s.annot from each subject in MNI space > in nii from. How can I obtain the Destrieux labels in nii format in > MNI (2mm) > How can I do this? > > Thank you, > Daiana > > > On Thu, Nov 9, 2017 at 1:36 PM, Bruce Fischl > <fis...@nmr.mgh.harvard.edu <mailto:fis...@nmr.mgh.harvard.edu>> wrote: > > Hi Daiana > > run mri_vol2vol --help. It has a bunch of examples and quite > extensive help > (thank you Doug!) > Bruce > > On Thu, 9 Nov 2017, Daya P wrote: > > > Hi Bruce, > > Can you give me some example code? I am not sure where the > talairach would go? > > > > > > On Thu, Nov 9, 2017 at 1:21 PM, Bruce Fischl > <fis...@nmr.mgh.harvard.edu <mailto:fis...@nmr.mgh.harvard.edu>> > wrote: > > Hi Daiana > > > > You should be able to use mri_vol2vol on the > aparc+aseg.mgz and the > > talairach.xfm in the subject's mri/transforms dir. > > > > cheers > > Bruce > > > > On Thu, 9 Nov 2017, Daya P wrote: > > > > > Hi All, > > > I processed a bunch of subjects using recon-all, but now > I would like to get labels > > from > > > aparc.a2009s.annot from each subject in MNI space in nii > from, the problem is that the > > annotation > > > file (lh and rh) is in subject native space. I have a > grey matter mask in MNI from > > each subject and > > > my goal is to have each label from aparc.a2009s.annot to > fit that mask. > > > How can I do this? > > > > > > Thank you, > > > Daiana > > > > > > > > _______________________________________________ > > 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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > _______________________________________________ > 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
