I used this command:
mri_label2vol --label rh_amy_aseg.label --temp ../mri/brainmask.mgz --o rh_amy_aseg.mgz
I don't know what registration matrix to use or how to generate one.
Amy
what as your label2vol command? specifically, you need to have the proper registration matrix, which is probably the problem. btw, you can use mri_label2vol to convert directly to nii.
doug
amyr@nmr.mgh.harvard.edu wrote:
Hi Freesurfers, I want to convert a freesurfer label (amygdala aseg) to a ROI (nii file?) that I can use (overlay) in SPM. I ran mri_label2vol and then mri_convert from .mgz to .nii However, the label looks a little off, and I am wondering if I need to do some sort of transformation since Freesurfer works with the Talairach and SPM works with the MNI. In SPM, I registered the BOLD images to the T1 structural image generated in Freesurfer (after running mri_convert .mgz to .img). Does this conversion require a transformation?
Thanks for your help.
Regards, Amy
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