How to apply atlas masks to normalized EPI images in SPM

Dear Experts,

I successfully normalized EPI images to spm12\toolbox\OldNorm\EPI.nii.
Based on some literature, normalization should work also without anatomical images and the results look good.

If I check the result with ‘MRIcro’ or the SPM tool ‘Check Reg’ by comparing it to an atlas, everything looks good:

However, the images are not exactly in the same space, especially since there is more empty space around the AAL3 atlas. Therefore, I cannot apply the masks to the data in a straightforward manner.

My question is probably rather simple: How do I now use Matlab/SPM (ideally in a scripted manner) to apply masks of the differen regions to the data?

Thank you!
Marco

Would this help?

https://andysbrainbook.readthedocs.io/en/latest/SPM/SPM_Short_Course/SPM_09_ROIAnalysis.html#using-the-command-line-for-roi-analysis

Thank you!

This script does not look like it is doing any sort of transformation. In this image I highlight Index 19 of AAL3 and it should end up at the border of the brain, not inside of it:

To again illustrate the problem again, here you see my data and the AAL3 atlas:

So you can see how much more empty space there is around the atlas than around spm12\toolbox\OldNorm\EPI.nii (which I used for normalization).

And I am looking for a way to apply the rois from the atlas to this data.