Nipoppy
Nipoppy is a lightweight framework for standardized organization and processing of neuroimaging-clinical datasets. Its goal is to help users adopt the FAIR principles and improve the reproducibility of studies.
The framework includes three components:
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A protocol for data organization, curation and processing, with steps that include the following:
- Organization of raw data, including conversion of raw DICOMs (or NIfTIs) to BIDS
- Processing of imaging data with existing or custom pipelines
- Tracking of data availability and processing status
- Extraction of imaging-derived phenotypes (IDPs) for downstream statistical modelling and analysis
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A specification for dataset organization that extends the Brain Imaging Data Structure (BIDS) standard by providing additional guidelines for tabular (e.g., phenotypic) data and imaging derivatives.
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A command-line interface and Python package that provide user-friendly tools for applying the framework. The tools build upon existing technologies such as the Apptainer container platform and the Boutiques descriptor framework. Several existing containerized pipelines are supported out-of-the-box, and new pipelines can be added easily by the user.
- We have also developed a web dashboard for interactive visualizations of imaging and phenotypic data availability.
3 maintainers
Metadata
3 maintainers
Release files for nipoppy 0.4.7
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Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| nipoppy-0.4.7.tar.gz | 4.4 MB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| nipoppy-0.4.7-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 4.5 MB
Release files / nipoppy-0.4.7.tar.gz
| Download URL | nipoppy-0.4.7.tar.gz |
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| Size | 4.4 MB |
| Tags | Source |
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Transparency logRelease files / nipoppy-0.4.7-py3-none-any.whl
| Download URL | nipoppy-0.4.7-py3-none-any.whl |
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| Size | 139.3 kB |
| Tags | Python 3 |
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