graynet
graynet: single-subject morphometric networks for neuroscience connectivity applications - Published in JOSS (2018)
Science Score: 93.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 7 DOI reference(s) in README and JOSS metadata -
✓Academic publication links
Links to: sciencedirect.com, joss.theoj.org -
○Committers with academic emails
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○Institutional organization owner
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✓JOSS paper metadata
Published in Journal of Open Source Software
Keywords
Scientific Fields
Repository
Subject-wise networks from structural MRI, both vertex- and voxel-wise features (thickness, GM density, curvature, gyrification)
Basic Info
- Host: GitHub
- Owner: raamana
- License: mit
- Language: Jupyter Notebook
- Default Branch: master
- Homepage: https://raamana.github.io/graynet/
- Size: 33.8 MB
Statistics
- Stars: 38
- Watchers: 4
- Forks: 8
- Open Issues: 7
- Releases: 7
Topics
Metadata Files
README.md
graynet
News
- Volumetric version of graynet is available now - check here
Overview
Individualized single-subject networks from T1-weighted magnetic resonance imaging (MRI) features such as: - vertex-wise features such as cortical thickness, gyrification and curavature - volumetric features such as gray matter density (T1w images) or metabolic uptake (PET) or another voxel-wise feature - Subcortical morphometric features - or any other similar feature distributed over a domain (cortex, or whole brain) to enable compuatation of inter-regional edge weights
Applicable for whenever network-level features are useful, among which common use cases are: - Biomarker development. - Brain-behaviour relationships (e.g. for the diagnosis and prognosis of many brain disorders such as Alzheimer's, Parkinson's, Schizophrenia and the like). - Aging (changes in network properties over age and their relations to other variables).
Docs: https://raamana.github.io/graynet/
Quick illustration:
Installation
pip install -U graynet
Citation
If you found any parts of graynet to be useful in your research, I'd appreciate if you could cite the software paper in JOSS below, as well as the methods paper that motivated the tool development in that order:
- Raamana et al., (2018). graynet: single-subject morphometric networks for neuroscience connectivity applications. Journal of Open Source Software, 3(30), 924, https://doi.org/10.21105/joss.00924
- Raamana, P. R., & Strother, S. C. (2020), “Does size matter? Relationship between predictive power of single subject morphometric networks to spatial scale and edge weight”, Brain Structure and Function, 225(8), 2475-2493. DOI: 10.1007/s00429-020-02136-0
- Raamana, P. R., Weiner, M. W., Wang, L., Beg, M. F., & Alzheimer's Disease Neuroimaging Initiative. (2015). Thickness network features for prognostic applications in dementia. Neurobiology of aging, 36, S91-S102. https://www.sciencedirect.com/science/article/pii/S0197458014005521
Owner
- Name: Pradeep Reddy Raamana
- Login: raamana
- Kind: user
- Location: Pittsburgh, PA
- Company: University of Pittsburgh
- Website: crossinvalidation.com
- Twitter: Raamana_
- Repositories: 114
- Profile: https://github.com/raamana
Neuroscientist trying to bridge the gap between clinic & computer science. Interests: Machine learning, Neuroimaging, Brain disorders, Informatics, Open science
JOSS Publication
graynet: single-subject morphometric networks for neuroscience connectivity applications
Authors
Rotman Research Institute, Baycrest Health Sciences, Toronto, ON, Canada
Rotman Research Institute, Baycrest Health Sciences, Toronto, ON, Canada, Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
Editor
Ariel Rokem
Tags
neuroscience network morphometry connectivity gray matter graph histogram freesurferGitHub Events
Total
- Watch event: 2
Last Year
- Watch event: 2
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Pradeep Reddy Raamana | r****a@g****m | 209 |
| Pradeep Reddy Raamana | p****a@r****g | 87 |
| Omer Faruk Gulban | o****n | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 25
- Total pull requests: 39
- Average time to close issues: 3 months
- Average time to close pull requests: 6 months
- Total issue authors: 11
- Total pull request authors: 3
- Average comments per issue: 2.36
- Average comments per pull request: 0.33
- Merged pull requests: 3
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 1
- Pull request authors: 0
- Average comments per issue: 0.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- raamana (11)
- jlhanson5 (4)
- qwfyuestc (2)
- minchulusa (1)
- jamesruffle (1)
- marivas-MRI (1)
- XinQi7788 (1)
- dpiccolomd (1)
- antogeo (1)
- madisonlewis323 (1)
- soichih (1)
Pull Request Authors
- pyup-bot (36)
- raamana (2)
- ofgulban (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 39 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 21
- Total maintainers: 1
pypi.org: graynet
Individualized single-subject networks from T1 mri features such as cortical thickness and gray matter density.
- Homepage: https://github.com/raamana/graynet
- Documentation: https://graynet.readthedocs.io/
- License: mit
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Latest release: 0.5.6
published almost 3 years ago
Rankings
Maintainers (1)
Dependencies
- hiwenet *
- networkx *
- nibabel *
- numpy *
- hiwenet *
- networkx *
- nibabel *
- numpy *
- plotly *
- scipy *
- actions/checkout v3 composite
- actions/setup-python v3 composite
- hiwenet *
- medpy *
- networkx *
- nibabel *
- numpy *
- pyradigm *
- scipy *