snirf2bids

Python package for generating BIDS-fNIRS files from SNIRF files

https://github.com/bunpc/snirf2bids

Science Score: 36.0%

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
✓
Academic publication links
Links to: zenodo.org
○
Academic email domains
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (11.0%) to scientific vocabulary

Keywords

bids fnirs snirf

Last synced: 6 months ago · JSON representation

Repository

Python package for generating BIDS-fNIRS files from SNIRF files

Basic Info

Host: GitHub
Owner: BUNPC
License: mit
Language: Python
Default Branch: main
Homepage:
Size: 10.2 MB

Statistics

Stars: 4
Watchers: 3
Forks: 6
Open Issues: 0
Releases: 6

Topics

bids fnirs snirf

Created almost 4 years ago · Last pushed about 1 year ago

Metadata Files

Readme License Citation

snirf2BIDS

Conveniently generate BIDS files from SNIRF files.

Installation

`pip install snirf2bids`

snirf2bids requires Python > 3.

Usage

SNIRF files with valid BIDS names can be converted into BIDS metadata text files.

For use with snirf2bids, a SNIRF file name must include at least the sub- and task- entitites and end in _nirs.snirf, i.e. sub-01_task-tapping_nirs.snirf.

Generate BIDS text files from a SNIRF file

If the listfiles parameter is empty, snirf2bids replaces all existing BIDS files with newly generated ones; otherwise, it replaces only the files specified in listfiles. The parameter retainoldinfo, with a default value of True, ensures that information in the existing scans and participants files is retained whenever a conflict occurs. python snirf2bids.snirf2bids('<path to snirf file>', 'outputpath = <folder to generate files in>', 'list_files =<list of BIDS files to replace>' , 'retain_old_info=True')

Generate BIDS text files from a SNIRF file or from all SNIRF files within a directory and its subdirectories

If the listfiles parameter is empty, snirf2bids replaces all existing BIDS files with newly generated ones; otherwise, it replaces only the files specified in listfiles. The parameter retainoldinfo, with a default value of True, ensures that information in the existing scans and participants files is retained whenever a conflict occurs. python snirf2bids.snirf2bids_recurse('<path to a directiory or path to snirf file>', 'list_files =<list of BIDS files to replace>', 'retain_old_info=True')

Export BIDS text files in JSON Format

python s = snirf2bids.snirf2json('<path to snirf file>') # Returns serialized JSON in which keys are filenames and values are their contents

Contributors

Developed by BU BME Senior Design Group 3 (2022): Christian Arthur, Jeonghoon Choi, Jiazhen Liu, Juncheng Zhang and the Boston University Neurophotonics Center.

@Christian Arthur :melon:
@Juncheng Zhang :tangerine:
@Jeonghoon Choi :pineapple:
@Jiazhen Liu :grapes:

This project exists thanks to:

Owner

Name: BUNPC
Login: BUNPC
Kind: organization

Repositories: 9
Profile: https://github.com/BUNPC

GitHub Events

Total

Watch event: 1
Push event: 15
Fork event: 1
Create event: 9

Last Year

Watch event: 1
Push event: 15
Fork event: 1
Create event: 9

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 2
Total pull requests: 18
Average time to close issues: about 1 month
Average time to close pull requests: 1 day
Total issue authors: 1
Total pull request authors: 5
Average comments per issue: 1.0
Average comments per pull request: 0.22
Merged pull requests: 16
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

sstucker (2)

Pull Request Authors

sstucker (6)
andyzjc (5)
chrsthur (3)
sreekanthkura7 (3)
ELISALJZ (1)

Top Labels

Issue Labels

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- pypi 96 last-month

Total dependent packages: 0
Total dependent repositories: 1
Total versions: 39
Total maintainers: 2

pypi.org: snirf2bids

To convert snirf file to bids format.

Homepage: https://github.com/BUNPC/snirf2bids
Documentation: https://snirf2bids.readthedocs.io/
License: MIT
Latest release: 0.8.7
published about 1 year ago

Versions: 39
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 96 Last month

Rankings

Dependent packages count: 10.0%

Forks count: 14.2%

Average: 19.7%

Dependent repos count: 21.7%

Downloads: 25.0%

Stargazers count: 27.8%

Maintainers (2)

sreekanthkura7 sstucker