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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