Hi. What I am asking probably could appear quite silly, but I am stuck in it and can't figure out a way to proceed.
I need a ventricle mask to include in the afni proc script and I can't use freesurfer. So I was following the path suggested in Example11b of afni proc. The example involves "template: TT27" and uses "atlas: TT_desai_dd_mpm+tlrc" to make the masks.
I instead need an atlas that is good for MNI152_2009 template. In a precedent discussion of the board, I read that it was suggested to use for this case the atlas: "aparc.a2009s+aseg_REN_all.nii.gz", which I downloaded (if there are better atlases than this one good news for me).
Anyway, here comes the silly stucking part: this atlas appears to be in different coordinate systems with respect to all the above. It is in +orig view instead of being as all the other atlases and templates in +tlrc view. So I don't know how to deal with it (I cannot visualize it in overlays with the MNI template, and I am not sure if I can use it to mask the template without doing a terrible mess, and I don't know how to bring it to +tlrc space because @auto_tlrc function seems to be designed for anatomies not atlases!)
Any clarification or advice about this would be appreciated. Thanks in advance.
Ms
<3