cohort_creator
Creates a neuroimaging cohort by aggregating data across datasets.
Science Score: 67.0%
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
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✓DOI references
Found 3 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
○Academic email domains
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○Scientific vocabulary similarity
Low similarity (17.5%) to scientific vocabulary
Repository
Creates a neuroimaging cohort by aggregating data across datasets.
Basic Info
- Host: GitHub
- Owner: neurodatascience
- License: mit
- Language: Python
- Default Branch: main
- Homepage: https://cohort-creator.readthedocs.io/en/latest/
- Size: 9.51 MB
Statistics
- Stars: 1
- Watchers: 5
- Forks: 2
- Open Issues: 45
- Releases: 3
Metadata Files
README.md
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Cohort creator
TL;DR
Creates a neuroimaging cohort by aggregating data across datasets.
Command line tool to:
- install a set of BIDS datalad datasets,
- get the data for a set of participants,
- copy the data to a new directory structure to create a "cohort".
It takes 2 files as input that should list:
- datasets to be included in the cohort
- subject in each dataset to be included in the cohort
Both of those files can be generated by the neurobagel query tool.
For examples of inputs TSV files see this page.
It outputs the cohort following the recommendations from the BIDS extension proposal 35.
Requirements
Operating system
It is recommended to use this package on a linux / Mac OS.
If you are on Windows, try using WSL (Windows Subsystem for Linux) to run this package: windows does not handle symbolic links well, and this package relies on symlinks. If you decided to go ahead anyway make sure you have got a LOT of disk space available.
More information here
Python dependencies
Make sure you have the following installed:
datalad and its dependencies:
if you are have anaconda / conda, it should be 'just' a matter of running
bash conda install -c conda-forge dataladBut check the installation instructions for more details.
Other dependencies are listed in the pyproject.toml file.
Installation
bash
pip install cohort_creator
Installation from source
bash
git clone https://github.com/neurodatascience/cohort_creator.git
cd cohort_creator
pip install .
Limitations
Cohorts can only be created by aggregating data from open BIDS datasets curated with datalad.
Dataset types
Only possible to get data from:
- raw
- mriqc
- fmriprep
Not yet possible to get freesurfer data via the cohort creator, though the data is available in the sourcedata folder of the fmriprep datasets.
Blind spots
It may be possible that that some metadata files (JSON, TSV) are not accessed over correctly if they are not in the root of the dataset or the same folder as the data file.
Contributors ✨
Thanks goes to these wonderful people (emoji key):
 Michelle Wang 🐛 🤔 📓 |
 Remi Gau ⚠️ 🚧 📖 🐛 💻 |
This project follows the all-contributors specification. Contributions of any kind welcome!
Owner
- Name: NeuroDataScience
- Login: neurodatascience
- Kind: organization
- Website: https://neurodatascience.github.io/
- Repositories: 24
- Profile: https://github.com/neurodatascience
Citation (CITATION.cff)
cff-version: 1.2.0
title: "cohort_creator"
version: 0.1.0
abstract:
"Creates a neuroimaging cohort by aggregating data across datasets."
message: "If you use this software, please cite it as below."
repository-code: "https://github.com/neurodatascience/cohort_creator.git"
contact:
- affiliation: "Origami lab, McGill University, Québec, Canada"
email: remi.gau@gmail.com
family-names: Gau
given-names: Rémi
authors:
- family-names: "Gau"
given-names: "Rémi"
orcid: "https://orcid.org/0000-0002-1535-9767"
affiliation: Origami lab, McGill University, Québec, Canada"
license: MIT
keywords:
- BIDS
- brain imaging data structure
- neuroimaging
- dataset
GitHub Events
Total
- Issues event: 3
- Delete event: 8
- Issue comment event: 20
- Push event: 10
- Pull request event: 18
- Pull request review event: 10
- Create event: 11
Last Year
- Issues event: 3
- Delete event: 8
- Issue comment event: 20
- Push event: 10
- Pull request event: 18
- Pull request review event: 10
- Create event: 11
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 22
- Total pull requests: 49
- Average time to close issues: about 2 months
- Average time to close pull requests: 8 days
- Total issue authors: 3
- Total pull request authors: 5
- Average comments per issue: 0.77
- Average comments per pull request: 0.35
- Merged pull requests: 34
- Bot issues: 0
- Bot pull requests: 35
Past Year
- Issues: 1
- Pull requests: 9
- Average time to close issues: N/A
- Average time to close pull requests: about 2 months
- Issue authors: 1
- Pull request authors: 2
- Average comments per issue: 0.0
- Average comments per pull request: 0.89
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 9
Top Authors
Issue Authors
- Remi-Gau (23)
- surchs (2)
- chabld (1)
Pull Request Authors
- pre-commit-ci[bot] (22)
- dependabot[bot] (21)
- Remi-Gau (17)
- github-actions[bot] (9)
- allcontributors[bot] (3)
- surchs (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 18 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 2
- Total maintainers: 1
pypi.org: cohort-creator
Creates a neuroimaging cohort by aggregating data across datasets.
- Homepage: https://github.com/neurodatascience/cohort_creator
- Documentation: https://cohort-creator.readthedocs.io/en/latest/
- License: MIT
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Latest release: 0.3.0
published almost 2 years ago