Fourier mask on template
The Fourier Mask that you define on a template during an alignment project describes the Fourier content of the template, not the one of the data particles. It does not reflect directly the missing wedge of the tomogram (which is indicated through the table on a particle by particle way).
In most cases, this parameter of the project can be generated trivially by passing a volume filled with ones. This indicates that the template passed in the same project (in direct space) is complete in the Fourier space.
You'll only need to pass a non-trivial map when the template has been generated in a way that includes unknown Fourier components. This might happen when you generate a template averaging many membrane proteins extracted from the same membrane. If the normal of the membrane is approximately constant (for instance, the contact area between two cells), the average has missing fourier components. In this case you need to adjust the project parameter useCC to the value 2 to ask Dynamo to consider the fourier components of the template marked as zero in the template fourier mask as unknown when comparing the template and the particle (which will have its own map of known and unknown Fourier coefficients).