[Freesurfer] Anatomy File Orientation Question

Hi all, I am trying to bring my FreeSurfer brainmask into SPM and then to coregister it (along with some ROIs from FreeSurfer) to the same subject's mprage already processed (coregistered to functional data) in SPM. To do this, I used: mri_convert brainmask.mgz brainmask.nii.gz (then used gunz

[Freesurfer] Anatomy File Orientation Question

Hi all, Sorry to re-post: I am trying to bring my FreeSurfer brainmask into SPM and then to coregister it (along with some ROIs from FreeSurfer) to the same subject's mprage already processed (coregistered to functional data) in SPM. To do this, I used: mri_convert brainmask.mgz brainmask.nii.