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 ( 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).

ENIGMA Cortical Quality Control Protocol 2.0 (April 2017)

The original ENIGMA Cortical QC protocol was updated in April 2017. While it does not create a departure from the former process and results, it will increase the ease of QC assessment. Thus, the QC 2.0 protocol may be used going forward but does not require any retroactive implementation.

ENIGMA3 – GWAS Meta Analysis of Cortical Thickness and Surface Area

For ENIGMA3, all participating ENIGMA sites will be extracting cortical measures using FreeSurfer software and the Image Processing Protocols outlined below.

ENIGMA Subcortical Segmentation Protocols for Disease Working Groups

These protocols allow disease working groups to extract and visually inspect subcortical structures using FreeSurfer, R and a number of customized HTML scripts. 


The success of subcortical volume analysis in disease and the remarkable GWAS discoveries lends itself to a more detailed look into subcortical structures

ENIGMA2 – GWAS Meta Analysis of Subcortical Volumes

Below are the image processing protocols for GWAS meta-analysis of subcortical volumes, aka the ENIGMA2 project.

ENIGMA1 – GWAS Meta Analysis of Hippocampal, Intracranial and Total Brain Volume

Below are the protocols from the ENIGMA pilot project (Stein et al., 2012, Nature Genetics):

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