Dear Christopher,

I just downloaded MCALT atlas and found that dorsal skull edge of the MCALT atlas images did not match the dorsal skull edge of MNI template included in SPM12 or WFU pick atlas.
i.e. Skull of [X, Y] = [0, 0]mm in MCALT atlas is 77mm (in Z axis), while the point in MNI is located 92mm in Z axis.
(attached image derived from SPM's "Check Reg")

I was wondering if there is anything worng with my files or MCALT atlas files.
Thanks for your help!

Best,
Yosuke

Hi Yosuke,
Thanks for your very detailed explanation of your question! The MCALT template/atlas boundaries are not intended to match MNI. This is essentially a full replacement for MNI space for use with older brains. If you are using MCALT with SPM, then you should use the MCALT TPM's, and SPM can then normalize images to MCALT space rather than MNI. Atlases that were designed in MNI space are not compatible with MCALT without transforming them first somehow to match the new space.

Does that help?
Best,
Chris

Dear Chris,

Thanks for your reply.
I totally misunderstood the space issue.
I appreciate your help!

Best,
Yosuke