Worked great! Thank you both very much.
I’ll give it a try and get back to you.
It almost looks as though the atlas is being registered to the original anat_t1.nii.
Are the anatomy slices in the 3d viewer taken from the normalized preop images (glanat.nii)? I have Preop MRI selected in the drop down of the Anatomy Slice controller. Is it possible that the atlas is being resliced into the original anat_t1 space?
Coregistration and normalization look good. No FSL routines were used. I used ANTs for coregistration and normalization. I have a single preop mri (anat_t1.nii) and a single postop mri (postop_tra.nii).
sorry for the broken link. image here
Thank you very much, Andy.
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