The ENIGMA-Shape pipeline provides a streamlined tool to perform fine-grained analysis of deep gray matter morphometry using standard brain MRI. The package uses a set of common templates, harmonized for use across datasets and studies. For ease of use, ENIGMA-Shape is built as an add-on for the popular FreeSurfer software, requiring few additional computations once MRI data has been processed with FreeSurfer’s “recon-all” pipeline. The package contains all the steps necessary for performing a shape study once an MR image has been parcellated into anatomical regions, including surface modeling, semi-automated quality control, and vertex-wise statistical analysis. Please see the ENIGMA Shape Analysis homepage for the distribution and documentation.