To create a single T1 weighted MRI template that can be used with FreeSurfer, you can use the following steps:

1. Preprocess your T1 weighted MRIs using SPM12, including steps such as bias correction, skull stripping, and spatial normalization.

2. Use the DARTEL toolbox in SPM12 to create a study-specific template from the preprocessed T1 weighted MRIs. When setting up the DARTEL process, make sure to select "Create Templates Only" and "None" for the tissue classes to create a single T1 weighted MRI template.

3. After creating the study-specific template, you can use it as input for FreeSurfer or any other software that requires a T1 weighted MRI template.

By following these steps, you should be able to generate a morphologically averaged template of T1 weighted MRIs that can be used with FreeSurfer or other software. If you continue to encounter issues, it may be helpful to consult the SPM12 documentation or seek assistance from other researchers familiar with these tools.