https://github.com/netneurolab/neuromaps

A toolbox for comparing brain maps
https://github.com/netneurolab/neuromaps

brain-imaging hacktoberfest neuroimaging python

Last synced: about 1 year ago
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A toolbox for comparing brain maps

• Host: GitHub
• URL: https://github.com/netneurolab/neuromaps
• Owner: netneurolab
• License: other
• Created: 2021-06-10T16:00:34.000Z (about 5 years ago)
• Default Branch: main
• Last Pushed: 2024-11-05T22:00:22.000Z (over 1 year ago)
• Last Synced: 2024-11-09T10:11:43.668Z (over 1 year ago)
• Topics: brain-imaging, hacktoberfest, neuroimaging, python
• Language: Python
• Homepage: https://netneurolab.github.io/neuromaps
• Size: 2.45 MB
• Stars: 244
• Watchers: 7
• Forks: 55
• Open Issues: 20
• Metadata Files:
  • Readme: README.rst
  • Contributing: docs/contributing.rst
  • License: LICENSE

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README

          
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The ``neuromaps`` toolbox is designed to help researchers make easy,

statistically-rigorous comparisons between brain maps (or brain annotations).

Documentation can be found `here `_.

The accompanying paper is published in `Nature Methods `_ (`postprint `_).

Check all the brain maps we have `here `_!

Features

--------

- A growing library of brain maps ("annotations") in their original coordinate space, including microstructure, function, electrophysiology, receptors, and more

- Robust transforms between MNI-152, fsaverage, fsLR, and CIVET spaces

- Integrated spatial null models for statistically assessing correspondences between brain maps

.. image:: https://github.com/netneurolab/neuromaps/raw/main/docs/_static/neuromaps_features.png

Installation requirements

-------------------------

Currently, ``neuromaps`` works with Python 3.8+.

You can install stable versions of ``neuromaps`` from PyPI with ``pip install neuromaps``.

However, we recommend installing from the source repository to get the latest features and bug fixes.

You can install ``neuromaps`` from the source repository with ``pip install git+https://github.com/netneurolab/neuromaps.git``

or by cloning the repository and installing from the local directory:

.. code-block:: bash

    git clone https://github.com/netneurolab/neuromaps

    cd neuromaps

    pip install .

You will also need to have `Connectome Workbench `_ installed and available on your path in

order to use most of the transformation / resampling functionality of

``neuromaps``.

.. _installation:

Citation

--------

**Importantly**, ``neuromaps`` implements and builds on tools that have been previously developed, and we redistribute data that was acquired elsewhere.

If you use the ``neuromaps`` toolbox, please ensure proper attribution of the original data sources. Here's a quick checklist:

- Cite the ``neuromaps`` `paper `_.

- Cite the original papers that publish the data you are using. A complete list with references for each brain annotation can be found `in the documentation `_, or `in this Google Sheet `_. We also provide a standalone bibliography file and a helper function to generate the citations.

- Cite the transformations used

  - Volume-to-surface transformations (registration fusion): `Buckner et al 2011 `_ (original proposition) and `Wu et al 2018 `_ (first implementation of MNI152 to fsaverage transformation).

  - Surface-to-surface transformations (multimodal surface matching): `Robinson et al 2014 `_ and `Robinson et al 2018 `_.

- Cite the spatial null models used (see API documentation)

License information

-------------------

This work is licensed under a

Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License ``cc-by-nc-sa``.

The full license can be found in the

`LICENSE `_ file in the ``neuromaps`` distribution.