https://github.com/mica-mni/enigma
The ENIGMA Toolbox is an open-source repository for accessing 100+ ENIGMA statistical maps, visualizing cortical and subcortical surface data, and relating neuroimaging findings to micro- and macroscale brain organization. 🤠
https://github.com/mica-mni/enigma
analysis awesome connectomics enigma life-changing-magic mri multiscale multisite neuroimaging open-source straight-fire visualization workflows
Last synced: 5 months ago
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The ENIGMA Toolbox is an open-source repository for accessing 100+ ENIGMA statistical maps, visualizing cortical and subcortical surface data, and relating neuroimaging findings to micro- and macroscale brain organization. 🤠
- Host: GitHub
- URL: https://github.com/mica-mni/enigma
- Owner: MICA-MNI
- License: bsd-3-clause
- Created: 2020-07-15T13:15:43.000Z (almost 5 years ago)
- Default Branch: master
- Last Pushed: 2024-04-11T14:02:16.000Z (about 1 year ago)
- Last Synced: 2024-04-11T17:01:45.265Z (about 1 year ago)
- Topics: analysis, awesome, connectomics, enigma, life-changing-magic, mri, multiscale, multisite, neuroimaging, open-source, straight-fire, visualization, workflows
- Language: Python
- Homepage: https://enigma-toolbox.readthedocs.io
- Size: 132 MB
- Stars: 113
- Watchers: 9
- Forks: 26
- Open Issues: 4
-
Metadata Files:
- Readme: README.rst
- Contributing: CONTRIBUTING.md
- License: LICENSE
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README
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.. image:: https://github.com/saratheriver/enigma-extra/blob/master/title.png?raw=true
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The **ENIGMA TOOLBOX** is an open source repository for (*i*) accessing 100+ ENIGMA-derived statistical maps, (*ii*)
visualizing and manipulating cortical and subcortical surface data, and (*iii*) contextualizing neuroimaging findings
at the microscale (using *postmortem* gene expression and cytoarchitecture) and macroscale (using structural and functional
connectome data).
.. image:: https://github.com/saratheriver/enigma-extra/blob/master/Figure0_GH3.png?raw=true
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:scale: 50%
Documentation 💼
---------------------------------------------
Check out our expandable online documentation at http://enigma-toolbox.readthedocs.io to learn how to:
| 🔌 install ENIGMA Toolbox in Python or Matlab
| 💯 load over 100 case-control datasets from several ENIGMA Working Groups
| 🥍 perform cross-disorder analyses
| 🚢 import your own data
| 🧩 map parcellated data to and from vertexwise space
| 🥡 export data and data results to several file formats
| 🧠 visualize and manipulate cortical and subcortical surface data
| 🔗 load preprocessed connectivity data from the Human Connectome Project (HCP)
| 🧬 load gene expression data from the Allen Human Brain Atlas
| 🎣 query pre-defined lists of disease-related genes from published GWAS
| 🔬 stratify neuroimaging findings according to BigBrain statistical moments and gradient
| 📱 stratify neuroimaging findings according to cytoarchitectural variations
| 🛩 build hub susceptibility models
| 📌 identify disease epicenters
| 🌪 perform spin permutation tests on parcellated data
|
Installation 🔨
---------------------------------------------
To install the Toolbox in ``Python``, run the following in your terminal:
.. code-block:: bash
git clone https://github.com/MICA-MNI/ENIGMA.git
cd ENIGMA
python setup.py install
|
To install the Toolbox in ``Matlab``, run the following in your terminal:
.. code-block:: bash
git clone https://github.com/MICA-MNI/ENIGMA.git
And then simply run the following in Matlab:
.. code-block:: matlab
addpath(genpath('/path/to/ENIGMA/matlab/'))
|
Acknowledgements 💕
----------------------------
Please acknowledge this work using the citation below:
Larivière, S., Paquola, C., Park, By. Royer, J., Wang, Y., Benkarim, O., Vos de Wael, R., Valk, S., Thomopoulos, S.I., Kirschner, M., Lewis, L.B., Evans, A.C., Sisodiya, S.M., McDonald, C.R., Thompson, P.T, Bernhardt, B.C.. The ENIGMA Toolbox: multiscale neural contextualization of multisite neuroimaging datasets. *Nat Methods* **18**, 698–700 (2021). https://doi.org/10.1038/s41592-021-01186-4
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