mni-to-atlas 0.3

A simple Python-based tool for finding brain atlas regions based on MNI coordinates.

mni_to_region

A simple Python-based tool for finding brain atlas regions based on MNI coordinates, with basic plotting abilities to show the sagittal, coronal, and axial views of the coordinates on the atlas.

Currently, the automated anatomical labelling (AAL) atlas [1] and AAL3 atlas [2] are supported.

Example screenshot of the plotting:

Requirements:

See here for the list of requirements.

Use Example:

1. Install the package into the desired environment using pip pip install -i https://test.pypi.org/simple/ mni-to-atlas
2. Import the AtlasBrowser class from mni_to_atlas into your workspace, e.g. from mni_to_atlas import AtlasBrowser
3. Create an instance of the AtlasBrowser class and specify an atlas to use, e.g. atlas = AtlasBrowser("AAL3")
4. Provide MNI coordinates to the AtlasBrowser object to find the corresponding atlas regions, e.g. regions = atlas.find_regions(coordinates), where coordinates is an [n x 3] numpy ndarray, where each row contains an x-, y-, and z-axis MNI coordinate. The regions output is a list of strings containing the region names for each set of coordinates
   • By default, plotting the coordinates is not performed, however this can be changed by setting plot = True in the find_regions method, e.g. atlas.find_regions(coordinates, plot=True). In this case, a figure will be generated for each set of coordinates

References:

1. Tzourio-Mazoyer et al. (2002), NeuroImage, 10.1006/nimg.2001.0978
2. Rolls et al. (2020), NeuroImage, 10.1016/j.neuroimage.2019.116189