https://github.com/coganlab/bids_coding
A conversion script designed to enable fast conversion of large neuro data sets
Science Score: 26.0%
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
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○Academic publication links
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○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (11.7%) to scientific vocabulary
Keywords
Repository
A conversion script designed to enable fast conversion of large neuro data sets
Basic Info
- Host: GitHub
- Owner: coganlab
- License: mit
- Language: Python
- Default Branch: main
- Homepage: https://bids-coding.readthedocs.io/en/latest/
- Size: 47.3 MB
Statistics
- Stars: 3
- Watchers: 1
- Forks: 4
- Open Issues: 17
- Releases: 0
Topics
Metadata Files
README.md
Work in Progress
See issues for updates on code completion progress
BIDS_coding
These scripts are intended for the creation and manipulation of BIDS compliant IEEG data set to the new specifications. Currently focused on EEG data type conversion, although multi-echo MRI data is also supported. For more conventional fMRI type BIDS conversions it is recommended you first look at BIDScoin as it has great general coverage than this repository.
Each python script can be run repreatedly using an iterator shell script like the one within the bids converter. They can also be run in the command line and will automatically iterate through a whole dataset if the top folder is indicated in the command.
BIDS_converter methodology is based off of this project
Dependencies
Software (as needed only): Afni, Freesurfer, Fsl, Anaconda (python 3.8)
Python packages:
boto3, pathlib, pybids, pydicom, nipype, pip, tedana, scipy
Optional python packages
Ubuntu packages:
dcm2niix, pigz
Host Requirements
Linux:
xauth
Mac:
xQuartz
The Lab
https://www.coganlab.org/
Owner
- Name: coganlab
- Login: coganlab
- Kind: organization
- Email: coganlab_github@googlegroups.com
- Location: United States of America
- Website: https://coganlab.pages.oit.duke.edu/wiki/
- Twitter: CoganLab
- Repositories: 6
- Profile: https://github.com/coganlab
GitHub Events
Total
- Watch event: 1
- Push event: 19
- Fork event: 2
- Create event: 3
Last Year
- Watch event: 1
- Push event: 19
- Fork event: 2
- Create event: 3
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 49
- Total pull requests: 56
- Average time to close issues: about 1 month
- Average time to close pull requests: 4 days
- Total issue authors: 3
- Total pull request authors: 3
- Average comments per issue: 0.45
- Average comments per pull request: 0.04
- Merged pull requests: 48
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 2
- Pull requests: 8
- Average time to close issues: N/A
- Average time to close pull requests: 6 minutes
- Issue authors: 1
- Pull request authors: 2
- Average comments per issue: 0.0
- Average comments per pull request: 0.0
- Merged pull requests: 6
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- Aaronearlerichardson (27)
- coganlab (1)
- jimzhang629 (1)
Pull Request Authors
- Aaronearlerichardson (36)
- jimzhang629 (2)
- TrellixVulnTeam (1)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- actions/checkout v2 composite
- actions/setup-python v2 composite
- actions/checkout v2 composite
- actions/setup-python v2 composite
- bids >=0.0
- exrex >=0.10.5
- matgrab >=0.0.8
- nibabel >=3.2.1
- numpy >=1.19.2
- pandas >=1.1.3
- pyEDFlib >=0.1.22
- pybids >=0.13
- pydicom >=2.1.2
- pytest *
- scipy <=1.6.2
- typing >=3.7.4