https://github.com/bbfrederick/capcalc
Various programs for processing and displaying coactivation patterns in fMRI data
Science Score: 36.0%
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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✓Committers with academic emails
2 of 4 committers (50.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (10.9%) to scientific vocabulary
Keywords from Contributors
interactive
projection
generic
sequences
archival
neuroimaging
embedded
genomics
observability
autograding
Last synced: 10 months ago
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JSON representation
Repository
Various programs for processing and displaying coactivation patterns in fMRI data
Basic Info
- Host: GitHub
- Owner: bbfrederick
- License: apache-2.0
- Language: Python
- Default Branch: main
- Size: 19.3 MB
Statistics
- Stars: 6
- Watchers: 2
- Forks: 3
- Open Issues: 0
- Releases: 20
Created over 9 years ago
· Last pushed 11 months ago
Metadata Files
Readme
Changelog
License
README.rst
Capcalc ======= capcalc is a suite of python programs used to perform coactivation pattern analysis on time series data. It uses K-Means clustering to find a set of “activation states” that represent the covarying patterns in the data. HTML documentation is here: http://capcalc.readthedocs.io/en/latest/ NOTE ==== This is an evolving code base. I’m constantly tinkering with it. That said, now that I’m releasing this to the world, I’m being somewhat more responsible about locking down stable release points. In between releases, however, I’ll be messing with things. **It’s very possible I could break something while doing this, so check back for status updates if you download the code in between releases**. I’ve finally become a little more modern and started adding automated testing, so as time goes by hopefully the “in between” releases will be somewhat more reliable. Check back often for exciting new features and bug fixes! Ok, I’m sold. What’s in here? ============================= - **roidecompose** - This program uses an atlas to extract timecourses from a 4D nifti file, producing a text file with the averaged timecourse from each region in the atlas (each integral value in file) in each column. This can be input to capfromtcs. There are various options for normalizing the timecourses. - **capfromtcs** - This does the actual CAP calculation, performing a k-means cluster analysis on the set of timecourses to find the best representitive set of “states” in the file. Outputs the states found and the dominant state in each timepoint of the timecourse. - **maptoroi** - The inverse of roidecompose. Give it a set of cluster timecourses and a template file, and it maps the values back onto the rois - **statematch** - Use this for aligning two state output files. Takes two state timecourse files, and determines which states in the second correspond to which states in the first. Generates a new ‘remapped’ file with the states in the second file expressed as states in the first.
Owner
- Name: Blaise deB Frederick
- Login: bbfrederick
- Kind: user
- Website: www.nirs-fmri.net
- Twitter: blaisefrederick
- Repositories: 4
- Profile: https://github.com/bbfrederick
MR Physicist who took a very wrong turn somewhere in the 80's, and ended up in psychiatry. Director of the Optomagnetic Group in the McLean Hospital BIC.
GitHub Events
Total
- Release event: 5
- Delete event: 9
- Issue comment event: 2
- Push event: 31
- Pull request event: 27
- Create event: 17
Last Year
- Release event: 5
- Delete event: 9
- Issue comment event: 2
- Push event: 31
- Pull request event: 27
- Create event: 17
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Blaise deB Frederick | b****k@g****m | 293 |
| Blaise Frederick | b****k@m****u | 154 |
| dependabot[bot] | 4****] | 27 |
| Daniel M. Drucker | d****r@m****u | 2 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 3
- Total pull requests: 72
- Average time to close issues: 4 days
- Average time to close pull requests: 9 days
- Total issue authors: 2
- Total pull request authors: 2
- Average comments per issue: 2.67
- Average comments per pull request: 0.22
- Merged pull requests: 54
- Bot issues: 0
- Bot pull requests: 70
Past Year
- Issues: 0
- Pull requests: 23
- Average time to close issues: N/A
- Average time to close pull requests: 4 days
- Issue authors: 0
- Pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 0.13
- Merged pull requests: 18
- Bot issues: 0
- Bot pull requests: 23
Top Authors
Issue Authors
- dmd (2)
- pstewa (1)
Pull Request Authors
- dependabot[bot] (82)
- dmd (2)
Top Labels
Issue Labels
bug (1)
Pull Request Labels
dependencies (82)
github_actions (63)
docker (19)
Packages
- Total packages: 1
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Total downloads:
- pypi 55 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 15
- Total maintainers: 1
pypi.org: capcalc
capcalc is a suite of python programs used to perform coactivation pattern analysis on time series data.
- Homepage: https://github.com/bbfrederick/capcalc
- Documentation: https://capcalc.readthedocs.io
- License: Apache Software License
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Latest release: 1.4.0
published over 1 year ago
Rankings
Dependent packages count: 6.6%
Downloads: 18.4%
Average: 19.1%
Forks count: 19.6%
Stargazers count: 20.5%
Dependent repos count: 30.6%
Maintainers (1)
Last synced:
11 months ago