The option -d indicates the dimension of the images provide, in this case all images were three-dimensional.  The -s option indicates that there will  be four iterations of this protocol performed. The other settings were included as standard procedure. Please see the user manual for ANTs for more information.

Template Generation

All of the preprocessed images were then used to generate a template. The template was created in two parts. The first part of the template included only affine normalization, and the second step included a full deformable registration. The first portion of the template was created using ANTs: