Re: [Freesurfer] Getting aparc.a2009s.annot in MNI

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

Re: [Freesurfer] Getting aparc.a2009s.annot in MNI

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?

Re: [Freesurfer] Getting aparc.a2009s.annot in MNI

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

Re: [Freesurfer] Getting aparc.a2009s.annot in MNI

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 wrote: > Hi Daiana > > You should be able to use mri_vol2vol on the aparc+aseg.mgz and the > talairach.xfm in the subject's

Re: [Freesurfer] Getting aparc.a2009s.annot in MNI

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 >

[Freesurfer] Getting aparc.a2009s.annot in MNI

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