Data

Tools

Indexes

Applications

Experiments

Open Source Science

https://github.com/tsbinns/mni_to_atlas

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

https://github.com/tsbinns/mni_to_atlas

Science Score: 39.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 9 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (10.6%) to scientific vocabulary

Keywords

aal aal3 brain-atlas brain-imaging brain-regions brain-visualization mni neuroimaging neuroscience python python3
Last synced: 6 months ago · JSON representation

Repository

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

Basic Info
  • Host: GitHub
  • Owner: tsbinns
  • License: mit
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 715 KB
Statistics
  • Stars: 11
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 3
Topics
aal aal3 brain-atlas brain-imaging brain-regions brain-visualization mni neuroimaging neuroscience python python3
Created over 3 years ago · Last pushed 7 months ago
Metadata Files
Readme Changelog License

README.md

mni-to-atlas

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.

The following atlases are currently supported: - Automated anatomical labelling atlas [1] - Automated anatomical labelling 3 atlas (1mm3 voxel version) [2] - Human Connectome Project extended parcellation atlas [3]

If there is an atlas you would like to see added, please open an issue.

Example screenshot of the plotting: image

Requirements:

See here for the list of requirements.

Use Example:

  1. Install the package into the desired environment using pip pip install mni-to-atlas.
  2. Import the AtlasBrowser class into your workspace.
  3. Create an instance of the AtlasBrowser class and specify an atlas to use (can be "AAL", "AAL3", or "HCPEx").
  4. Provide MNI coordinates to the AtlasBrowser object to find the corresponding atlas regions. The brain regions for these coordinates are then returned as a list of strings.
    • The coordinates should be an (n x 3) array, where each row contains an x-, y-, and z-axis MNI coordinate.
    • By default, plotting the coordinates is not performed, however this can be changed by setting plot = True in the find_regions method. In this case, a figure will be generated for each set of coordinates.


```python

Import the AtlasBrowser class

from mnitoatlas import AtlasBrowser

Instantiate the AtlasBrowser class and specify the atlas to use

atlas = AtlasBrowser("AAL3")

Provide MNI coordinates as an (n x 3) array

coordinates = np.array([[-24, -53, 73], [-25, 20, 78]])

Find the brain regions at the MNI coordinates (plotting is optional)

regions = atlas.find_regions(coordinates, plot=True) ```

References:

  1. Tzourio-Mazoyer et al. (2002) DOI: 10.1006/nimg.2001.0978
  2. Rolls et al. (2020) DOI: 10.1016/j.neuroimage.2019.116189
  3. Huang et al. (2022) DOI: 10.1007/s00429-021-02421-6

Owner

  • Name: Thomas Samuel Binns
  • Login: tsbinns
  • Kind: user
  • Location: Berlin, Germany
  • Company: Deptartment of Neurology, Charité - Universitätsmedizin Berlin

Ph.D. Neuroscience Fellow; M.Sci. Neuroscience with Psychology graduate. Interested in computational, cognitive, and translational neuroscience.

GitHub Events

Total
  • Release event: 1
  • Watch event: 1
  • Issue comment event: 3
  • Create event: 1
Last Year
  • Release event: 1
  • Watch event: 1
  • Issue comment event: 3
  • Create event: 1

Committers

Last synced: 8 months ago

All Time
  • Total Commits: 36
  • Total Committers: 1
  • Avg Commits per committer: 36.0
  • Development Distribution Score (DDS): 0.0
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Thomas Samuel Binns t****s@o****m 36

Issues and Pull Requests

Last synced: 8 months ago

All Time
  • Total issues: 3
  • Total pull requests: 0
  • Average time to close issues: 6 months
  • Average time to close pull requests: N/A
  • Total issue authors: 3
  • Total pull request authors: 0
  • Average comments per issue: 1.67
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • SaraDadjouy (1)
  • caggursoy (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 184 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 7
  • Total maintainers: 1
pypi.org: mni-to-atlas

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

  • Versions: 7
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 184 Last month
Rankings
Dependent packages count: 6.6%
Average: 18.6%
Dependent repos count: 30.6%
Maintainers (1)
tsbinns
Last synced: 6 months ago

Dependencies

pyproject.toml pypi
  • matplotlib >= 3.5
  • nibabel >= 3.2
  • numpy >= 1.22
requirements.txt pypi
  • matplotlib ==3.5.1
  • nibabel ==3.2.2
  • numpy ==1.22.3