m2g
NeuroData's MRI to Graphs (m2g) - connectome estimation package and pipeline
Science Score: 46.0%
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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✓DOI references
Found 5 DOI reference(s) in README -
✓Academic publication links
Links to: biorxiv.org, zenodo.org -
✓Committers with academic emails
15 of 38 committers (39.5%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (16.5%) to scientific vocabulary
Keywords from Contributors
Repository
NeuroData's MRI to Graphs (m2g) - connectome estimation package and pipeline
Basic Info
- Host: GitHub
- Owner: neurodata
- License: other
- Language: Python
- Default Branch: deploy
- Homepage: https://docs.neurodata.io/m2g/
- Size: 89 MB
Statistics
- Stars: 63
- Watchers: 10
- Forks: 37
- Open Issues: 29
- Releases: 4
Metadata Files
README.md
m2g
NeuroData's MR Graphs package, m2g, is a turn-key pipeline which uses structural and diffusion MRI data to estimate multi-resolution connectomes reliably and scalably.
Contents
Overview
The m2g pipeline has been developed as a beginner-friendly solution for human connectome estimation by providing robust and reliable estimates of connectivity across a wide range of datasets. The pipelines are explained and derivatives analyzed in our pre-print, available on BiorXiv.
Documentation
Check out some resources on our website, or our function reference for more information about m2g.
System Requirements
Hardware Requirements
m2g pipelines requires only a standard computer with enough RAM (< 16 GB).
Software Requirements
The m2g pipeline:
- was developed and tested primarily on Mac OS (10,11), Ubuntu (16, 18, 20), and CentOS (5, 6);
- made to work on Python 3.7-3.10;
- is wrapped in a Docker container;
- has install instructions via a Dockerfile;
- requires no non-standard hardware to run;
- has key features built upon FSL, AFNI, INDI, Dipy, Nibabel, Nilearn, Networkx, Numpy, Scipy, Scikit-Learn, and others
- For Python package version numbers, see requirements.txt
- For binaries required to install AFNI, FSL, INDI, ICA_AROMA, see the Dockerfile
- takes approximately 1-core, < 16-GB of RAM, and 1-2 hours to run for most datasets (varies based on data).
Installation
Instructions can be found within our documentation: https://docs.neurodata.io/m2g/install.html
Usage
Instructions can be found within our documentation and a demo can be found here.
License
This project is covered under the Polyform License.
Issues
If you're having trouble, notice a bug, or want to contribute (such as a fix to the bug you may have just found) feel free to open a git issue or pull request. Enjoy!
Citing m2g
If you find m2g useful in your work, please cite the package via the m2g paper
Chung, J., Lawrence, R., Loftus, A., Kiar, G., Bridgeford, E. W., Roncal, W. G., Chandrashekhar, V., ... & Consortium for Reliability and Reproducibility (CoRR). (2024). A low-resource reliable pipeline to democratize multi-modal connectome estimation and analysis. bioRxiv, 2024-04.
Owner
- Name: neurodata
- Login: neurodata
- Kind: organization
- Email: admin@neurodata.io
- Location: everywhere
- Website: https://neurodata.io
- Repositories: 175
- Profile: https://github.com/neurodata
GitHub Events
Total
- Watch event: 2
Last Year
- Watch event: 2
Committers
Last synced: 11 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Disa Mhembere | d****1@j****u | 1,352 |
| gkiar | g****7@g****m | 1,095 |
| dPys | d****r@u****u | 209 |
| Disa Mhembere | d****a@j****u | 154 |
| Alex Loftus | a****4@g****m | 126 |
| Eric Bridgeford | e****2@j****u | 113 |
| Will Gray Roncal | w****r@j****u | 86 |
| Randal Burns | r****l@c****u | 81 |
| Disa Mhembere | d****1@g****m | 32 |
| Ross Lawrence | 5****s | 26 |
| gkiar | g****r@j****u | 24 |
| Jaewon Chung | j****8@g****m | 19 |
| Derek Pisner | 1****s | 13 |
| Daniel Sussman | d****3@j****u | 10 |
| William Gray Roncal | w****y@j****u | 6 |
| Eric Perlman | e****c@y****m | 6 |
| = | = | 6 |
| joshua vogelstein | j****v@j****u | 4 |
| Daniel Sussman | d****s@g****m | 4 |
| Disa | d****a@b****) | 4 |
| Dav Clark | C****a@k****g | 3 |
| Yaroslav Halchenko | d****n@o****m | 2 |
| Disa | d****a@b****) | 2 |
| Disa Mhembere | d****a@a****u | 2 |
| Disa Mhembere | d****a@b****) | 2 |
| randal | r****l@r****) | 2 |
| Vikram Chandrashekhar | v****6@j****u | 2 |
| Randal Burns | r****l@d****u | 2 |
| Joshua Vogelstein | j****o@o****l | 2 |
| Greg Kiar | g****r@c****u | 2 |
| and 8 more... | ||
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 7 months ago
All Time
- Total issues: 32
- Total pull requests: 77
- Average time to close issues: 11 months
- Average time to close pull requests: about 1 month
- Total issue authors: 15
- Total pull request authors: 10
- Average comments per issue: 1.38
- Average comments per pull request: 1.09
- Merged pull requests: 47
- Bot issues: 0
- Bot pull requests: 3
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
Top Authors
Issue Authors
- loftusa (7)
- luochuankai-JHU (3)
- JialinKang (3)
- j1c (3)
- wilttang (2)
- CaseyWeiner (2)
- XueminZhu-Charmaine (2)
- FangCai-fifi (2)
- Lawreros (2)
- KevinFCasey (1)
- mkoohim (1)
- davclark (1)
- PSSF23 (1)
- huzhen965278384 (1)
- ebridge2 (1)
Pull Request Authors
- Lawreros (21)
- j1c (16)
- loftusa (16)
- JialinKang (14)
- FangCai-fifi (7)
- dependabot[bot] (5)
- wilttang (3)
- luochuankai-JHU (2)
- PSSF23 (1)
- huzhen965278384 (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- pypi 17 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 1
- Total maintainers: 1
pypi.org: m2g
Neuro Data MRI to Graphs Pipeline
- Homepage: https://github.com/neurodata/m2g
- Documentation: https://m2g.readthedocs.io/
- License: other
-
Latest release: 0.3.0
published about 6 years ago
Rankings
Maintainers (1)
Dependencies
- sphinx *
- sphinx_rtd_theme *
- PyBASC ==0.4.5
- awscli ==1.15.40
- boto3 ==1.7.37
- click ==6.7
- configparser >=3.7.4
- cython *
- dipy ==1.1.1
- duecredit *
- fury ==0.5.1
- future ==0.16.0
- graspologic *
- hyppo ==0.1.3
- ipython *
- lockfile ==0.12.2
- matplotlib ==3.1.3
- networkx ==2.4
- nibabel ==3.2.2
- nilearn ==0.4.1
- nipype ==1.1.2
- nose ==1.3.7
- numba ==0.52.0
- numpy ==1.20.1
- pandas ==1.3.1
- pathlib ==1.0.1
- pathlib2 *
- patsy ==0.5.0
- plotly ==1.12.1
- prov ==1.5.0
- psutil ==5.6.6
- pybids ==0.12.0
- pytest *
- python-dateutil ==2.7.3
- pyvtk *
- regex *
- requests ==2.21.0
- scikit-image *
- scikit-learn ==0.22.1
- scipy >=0.13.3
- setuptools ==57.5.0
- traits ==4.6.0
- virtualenv *
- vtk *
- xvfbwrapper *
- yamlordereddictloader ==0.4.0
- awscli *
- boto3 *
- configparser >=3.7.4
- dipy >=1.0.0
- fury ==0.5.1
- matplotlib *
- networkx >=2.4
- nibabel *
- nilearn *
- numpy *
- plotly *
- pybids >=0.9.0
- pytest *
- pyvtk *
- requests *
- scikit-image *
- scipy *
- vtk *
- neurodebian bionic-non-free build