Screen Shot 2015-04-16 at 1.25.01 PMOur GWAS of subcortical structures (Hibar et al., 2015) are available for bulk download here.

To build on our successful first project studying the genetic influences on hippocampal volume, there is overwhelming support from current and new ENIGMA sites to examine the whole set of seven subcortical structures segmented by both FreeSurfer and FSL FIRST: caudate, putamen, pallidum, thalamus, accumbens, amygdala (and hippocampus with a larger sample size). This large number of structures to analyze is not as daunting as it may first appear. Using lessons from our first ENIGMA analysis, we have streamlined the processing pipeline and provide new tools that make the most time-consuming step of quality checking segmentation data quick and painless.

To complete this next project efficiently, we propose to complete the analysis in two stages: image processing and association analysis. The first stage of image processing, for most sites, will be nearly complete as each of the major segmentation programs (FSL and FreeSurfer) outputs the full set of subcortical structures required for this ENIGMA study. The next step of the image processing protocol is to perform quality checks of your data to exclude poorly segmented volumes. The quality checking process is streamlined as we provide (and have tested at several sites) a new protocol with tools to perform quick and effective checks of the segmentations.

This process was developed with advice and guidance from the developers of the segmentation methods. For example, detailed quality checking of all subcortical structures in 740 subjects from the ADNI study took approximately 5 days for one researcher to complete.

Given these considerations, we would like to set a preliminary goal of having each site complete the image processing stage by April 2012.

  • Protocols detailing each of the steps for completing the image processing steps may be found here: Imaging Protocols
  • Protocols detailing each of the steps for completing the imputation to the 1000 Genomes reference set may be found here: Genetics Protocols

Also, we thank Roberto Toro, Gunter Schumann, Mark Jenkinson, Neda Jahanshad, Katharina Whittfeld, Hans Grabe, Benjamin Aribisala, and Joanna Wardlaw for “beta” testing the new imaging protocols at their sites.

If you have any questions about the ENIGMA2 subcortical project, please email Derrek Hibar, Miguel Renteria, or Roberto Toro (

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