I'm not familiar with that template, and you haven't stated whether you preprocess the data via the SPMmouse toolbox or with SPM just relying on the template included in that toolbox. However, as segmentation seems to have worked well, what about the following steps:
- Segment (as there have been improvements with regard to the algorithm I'd suggest to turn to SPM12, the previously known "New Segment" has become the default "Segment" in SPM12, as stated with some adjustments)
- Dartel tools \ Initial Import \ specify the _sn.mat files
- Dartel tools \ Run Dartel (create Templates) \ load the files obtained from the previous step
During the 2nd step there's an option to adjust the bounding box and voxel size, this way you should be able to control the dimensions/size of the rc1, rc2 files created during that step (in contrast to the "Datel imported" ones obtained via Segment, for that step to work properly it would be necessary to trace back where the default settings come from). I can't gurantee the procedure to work, but it should be worth a try.