Dear Bas,
the only template of the substania nigra I know of is included in the "FSL Harvard-Oxford Probabilistic atlas of human cortical and subcortical brain areas". See FSL forum for the labels included https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0911&L=FSL&D=0&P=415578
There are non-FSL versions around as well, probably derived of the FSL version. PyROI https://github.com/mwaskom/PyROI/tree/master/data/HarvardOxford includes two nii files, but none of them seems to contain the SN. Donald McLaren's peak_nii toolbox has a corresponding nii file as well, but again no SN.
Best,
Helmut
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