I am trying to access the Paxinos atlas in NMT2 but I can’t find it. Do you know what the problem might be?
There is no “Paxinos” atlas in NMT2, as far as I know. The NMT installation script includes the NMT2 template and the CHARM atlases for now. It will soon integrate the SARM subcortical atlas too (Paxinos was a coauthor of that) that is available separately here:
Let me know if that helps or if you need something else.
Thanks for your reply!
I already have the CHARM/SARM in NMT2
A Paxinos atlas in NMT2 (in addition to the SARM and CHARM atlases) is mentioned here: https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/nonhuman/macaque_tempatl/template_nmtv2.html
This is why I was asking
You are correct, and I completely forgot about this. Ben Jung let me know that this was a warp of the DTI atlas from Calabrese et al., 2015, but it is not manually corrected. We didn’t really feel it was good enough quality for distribution, so that page will be updated to remove the Paxinos section. Ben still has that dataset if you really need that. Please let us know.