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It's useful to have all volumes in the mri directory, rather than their own atlases directory, because it facilitates things like warping subjects to digitization (MNE for example warps an mri/*.mgz). So if instead of putting them in atlases we can make them mgz with something like:
mri_convert atlases/brain_ANTS_IXI_atlas_head_space.nii.gz mri/brain_ANTS_IXI_atlas_head_space.mgz
then things work at the MNE end like they should.
Not sure if it's worth cutting a 0.2 just for this but it's probably worth adding to the scripts. I can make a PR for this if you want @christian-oreilly
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