Hi Marco,
I had a different issue but maybe the approach is similar: Using ROIs created by SPM with fMRIPrep data
In brief, you could try using ANTs or FSL to compute registration parameters between the template that your atlas is based on and the template that you used to register you data to and then apply the resulting transformation parameters to your atlas-based ROIs. At least for my issue, this worked.
Best,
Jasmin