ENIGMA Protocol for the Segmentation of Subcortical Structures

Please find here the suggested protocols for the imaging analysis part of the ENIGMA project.  These protocols are to be used as a suggestion and other validated software to perform these analyses may be used as well.

Anyone is welcome to use these protocols for their projects! If you use the protocols on this site for projects outside of ENIGMA, please include a reference to the ENIGMA main page (http://enigma.loni.ucla.edu/) so that your readers and reviewers know about it as well. Please also reference the ENIGMA publication if you are using the ENIGMA1 protocols (Stein et al., 2012, Nature Genetics).

• Step 1: Segmentation of subcortical structures with FIRST
• Step 2: Extract volume values for further analysis (FreeSurfer Users Start Here)
• Step 3: Quality checking subcortical structures
• Step 4: Generate summary statistics and histogram plots