Welcome to the ENIGMA TOOLBOX 👋🏼



100+ ENIGMA-derived statistical maps 💯

The ENIGMA TOOLBOX provides a centralized, and continuously updated, repository of meta-analytical case-control comparisons across a wide range of disorders. As many ENIGMA groups have moved beyond meta-analysis towards ‘mega’-analysis of subject-level data, the ENIGMA TOOLBOX also includes an example of subject-level example data from an individual site that have been processed according to ENIGMA protocols. It should be noted, however, that subject-level or raw imaging data are not openly available for dissemination to the scientific community. Interested scientists are encouraged to visit the ENIGMA website to learn more about current projects, joining and contributing to an active Working Group, or proposing a new group.


Compatible with any neuroimaging datasets and software 💌

To increase generalizability and usability, every function within the ENIGMA TOOLBOX is also compatible with typical neuroimaging datasets parcellated according to the Desikan-Killiany, Glasser, and Schaefer parcellations.

To simplify things, we provide tutorials on how to (i) import vertexwise and/or parcellated data, (ii) parcellate vertexwise cortical data, (iii) map parcellated data to the surface, and (iv) export data results. Import/export file formats include: .txt/.csv, FreeSurfer/”curv”. mgh/.mgz, GIfTI/.gii, and CIfTI/.dscalar.nii/.dtseries.nii. Cortical and subcortical surfaces are also available in FreeSurfer/surface, GIfTI/.gii, .vtk, and .obj formats, allowing cross-software compatibility.


Cortical and subcortical visualization tools 🎨

Tired of displaying your surface findings in tables? Look no further! The ENIGMA TOOLBOX has got you covered! Check out our visualization tools to project cortical and subcortical data results to the surface and generate publication-ready figures.


Preprocessed micro- and macroscale data 🤹🏼‍♀️

The emergence of open databases yields new opportunities to link human gene expression, cytoarchitecture, and connectome data. As part of the ENIGMA TOOLBOX, we have generated and made available a range of preprocessed and parcellated data, including: (i) transcriptomic data from the Allen Human Brain Atlas, (ii) cytoarchitectural data from the BigBrain Project, (iii) a digitized parcellation of the von Economo and Koskinas cytoarchitectonic map, and (iv) functional and structural connectivity data from the Human Connectome Project.


Multiscale analytical workflows 🦾

The ENIGMA Toolbox comprises two neural scales for the contextualization of findings: (i) using microscale properties, namely gene expression and cytoarchitecture, and (ii) using macroscale network models, such as regional hub susceptibility analysis and disease epicenter mapping. Moreover, our Toolbox includes non-parametric spatial permutation models to assess statistical significance while preserving the spatial autocorrelation of parcellated brain maps. From these comprehensive workflows, users can gain a deeper understanding of the molecular, cellular, and macroscale network organization of the healthy and diseased brains.


Step-by-step tutorials 👣

The ENIGMA TOOLBOX includes ready-to-use and easy-to-follow code snippets for every functionality and analytical workflow! Owing to its comprehensive tutorials, detailed functionality descriptions, and visual reports, the ENIGMA TOOLBOX is easy to use for researchers and clinicians without extensive programming expertise.


Development and getting involved ⚙️

Should you have any problems, questions, or suggestions about the ENIGMA TOOLBOX, please do not hesitate to post them to our mailing list! Are you interested in collaborating or sharing your ENIGMA-related data/codes/tools? Noice! Make sure you familiarize yourself with our contributing guidelines first and then discuss your ideas on our Github issues and pull request.





Core developers 👩🏻‍💻

  • Sara Larivière, MICA Lab - Montreal Neurological Institute
  • Boris Bernhardt, MICA Lab - Montreal Neurological Institute