Dear Katharina,
> Do you know if the coordinates in the SPM output are bregma coordinates when I use SPMMouse?
I would contact the author in your case, as they refer to some older conference contributions, and not all of them seem to be publically available. But in the meantime it should be sufficient to load the SPMMouse template nii and check whether the origin corresponds to the bregma and whether the coordinates e.g. along anterior-posterior match those of the Paxinos atlas.
> if I need a mask for a certain brain region?
Looking at Fig. 1 and 5 in Sawiak et al. (2009) they have delineated / reconstructed some anatomical structures, maybe they can be obtained from the authors.
But leaving this aside, Ma et al. (2014, PLOS ONE, https://dx.doi.org/10.1371/journal.pone.0086576 ) might be helpful. They describe an automatic paracellation of the mouse brain, and the labels are available from http://cmic.cs.ucl.ac.uk/staff/da_ma/Multi_Atlas/ and are in compatible format. The labels seem to be based on/take into account another atlas http://brainatlas.mbi.ufl.edu/ , possibly also a second atlas http://www.bioeng.nus.edu.sg/cfa/mouse_atlas.html . Details should be described in the paper, in any case the latter two also have SPM-compatible labels.
Very likely orientations and resolutions don't match those of SPMMouse brain, but assuming the average mouse brains in the different toolboxes/atlases are reasonably close to the Paxinos atlas and also to each other (which one would have to infer based on all the included data), then rotations, translations and resizing along the three dimensions should bring them into alignment.
Hope this helps a little
Helmut
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