https://github.com/aramis-lab/clinica-pydra-freesurfer
Pydra tasks for FreeSurfer designed for Clinica
Science Score: 13.0%
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
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○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 (9.2%) to scientific vocabulary
Keywords
Repository
Pydra tasks for FreeSurfer designed for Clinica
Basic Info
- Host: GitHub
- Owner: aramis-lab
- License: apache-2.0
- Language: Python
- Default Branch: main
- Homepage: https://aramis-lab.github.io/clinica-pydra-freesurfer/
- Size: 304 KB
Statistics
- Stars: 5
- Watchers: 4
- Forks: 1
- Open Issues: 2
- Releases: 12
Topics
Metadata Files
README.md
clinica-pydra-freesurfer
Pydra tasks for FreeSurfer designed for Clinica.
Pydra is a dataflow engine which provides a set of lightweight abstractions for DAG construction, manipulation, and distributed execution.
FreeSurfer is a neuroimaging toolkit for processing, analyzing, and visualizing human brain MR images.
This project exposes some of FreeSurfer's utilities as Pydra tasks to facilitate their integration into more advanced processing workflows.
Available interfaces
| Module | Interfaces | |-----------|-----------------------------------------------------------------------------------------------------| | gtmseg | GTMSeg | | mri | Aparc2Aseg, Binarize, Convert, Coreg, Label2Vol, RobustRegister, RobustTemplate, Surf2Surf, Vol2Vol | | mris | AnatomicalStats, CALabel, CATrain, Expand, Preproc | | recon_all | ReconAll, BaseReconAll, LongReconAll |
Installation
console
pip install clinica-pydra-freesurfer
A separate installation of FreeSurfer is required to use this package. Please review the following instructions and licensing details.
Development
This project is managed with Hatch:
console
pipx install hatch
To run the test suite:
console
hatch run test
To fix linting issues:
console
hatch fmt
To check the documentation:
console
hatch run docs:serve --open-browser
Licensing
This project is distributed under the terms of the Apache License, Version 2.0.
Owner
- Name: ARAMIS Lab
- Login: aramis-lab
- Kind: organization
- Location: Paris, France
- Website: www.aramislab.fr
- Twitter: AramisLabParis
- Repositories: 21
- Profile: https://github.com/aramis-lab
The Aramis Lab is a joint research team between CNRS, Inria, Inserm and Sorbonne University and belongs to the Paris Brain Institute (ICM).
GitHub Events
Total
- Member event: 1
- Create event: 2
Last Year
- Member event: 1
- Create event: 2
Issues and Pull Requests
Last synced: 6 months ago
Packages
- Total packages: 1
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Total downloads:
- pypi 10 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 1
- Total maintainers: 3
pypi.org: clinica-pydra-freesurfer
Pydra tasks for FreeSurfer designed for Clinica
- Documentation: https://aramis-lab.github.io/clinica-pydra-freesurfer
- License: Apache Software License
-
Latest release: 0.1.0
published almost 2 years ago
Rankings
Maintainers (3)
Dependencies
- pydra ^0.19
- python ^3.7
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- actions/checkout v3 composite
- actions/setup-python v4 composite
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- actions/checkout v3 composite
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