| Name | pydra-dcm2bids JSON |
| Version |
0.0.4
JSON |
| download |
| home_page | |
| Summary | Pydra tasks for dcm2bids |
| upload_time | 2023-03-19 18:58:36 |
| maintainer | |
| docs_url | None |
| author | |
| requires_python | >=3.7 |
| license | |
| keywords |
bids
dicom
pydra
|
| VCS |
|
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# pydra-dcm2bids
[![PyPI - Version][pypi-version]][pypi-project]
[![PyPI - Python Version][pypi-pyversions]][pypi-project]
----
Pydra tasks for dcm2bids.
[Pydra][pydra] is a dataflow engine which provides
a set of lightweight abstractions for DAG
construction, manipulation, and distributed execution.
[`dcm2bids`][dcm2bids] is a tool which facilitates
conversion from DICOM datasets to NIfTI files
organized as [BIDS][bids].
## Installation
```console
pip install pydra-dcm2bids
```
A separate installation of `dcm2bids` and `dcm2niix` is required to use this package.
Please review the following [instructions][dcm2bids-install].
`dcm2bids` can be installed alongside `pydra-dcm2bids` with:
```console
pip install 'pydra-dcm2bids[all]'
```
## Usage
```python
from pydra.tasks import dcm2bids
task = dcm2bids.Dcm2Bids(
dicom_dir="/path/to/dicom/dir",
output_dir="/path/to/bids/dir",
config_file="/path/to/config/file.json",
participant_id="sub-01",
)
result = task()
```
You may check the following example of a [configuration file][dcm2bids-config-file].
## Development
This project is managed with [Hatch][hatch]:
```console
pipx install hatch
```
To run the test suite:
```console
hatch run test:no-cov
```
To fix linting issues:
```console
hatch run lint:fix
```
To check the documentation:
```console
hatch run docs:serve --open-browser
```
## License
`pydra-dcm2bids` is distributed under the terms of the [Apache License, Version 2.0][license].
[pypi-project]: https://pypi.org/project/pydra-dcm2bids
[pypi-version]: https://img.shields.io/pypi/v/pydra-dcm2bids.svg
[pypi-pyversions]: https://img.shields.io/pypi/pyversions/pydra-dcm2bids.svg
[pydra]: https://pydra.readthedocs.io/
[dcm2bids]: https://unfmontreal.github.io/Dcm2Bids/
[bids]: https://bids-specification.readthedocs.io/
[dcm2bids-install]: https://unfmontreal.github.io/Dcm2Bids/docs/get-started/install/
[dcm2bids-config-file]: https://unfmontreal.github.io/Dcm2Bids/docs/how-to/create-config-file/
[hatch]: https://hatch.pypa.io/
[license]: https://spdx.org/licenses/Apache-2.0.html
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"description": "# pydra-dcm2bids\n\n[![PyPI - Version][pypi-version]][pypi-project]\n[![PyPI - Python Version][pypi-pyversions]][pypi-project]\n\n----\n\nPydra tasks for dcm2bids.\n\n[Pydra][pydra] is a dataflow engine which provides\na set of lightweight abstractions for DAG\nconstruction, manipulation, and distributed execution.\n\n[`dcm2bids`][dcm2bids] is a tool which facilitates\nconversion from DICOM datasets to NIfTI files\norganized as [BIDS][bids].\n\n## Installation\n\n```console\npip install pydra-dcm2bids\n```\n\nA separate installation of `dcm2bids` and `dcm2niix` is required to use this package.\nPlease review the following [instructions][dcm2bids-install].\n\n`dcm2bids` can be installed alongside `pydra-dcm2bids` with:\n\n```console\npip install 'pydra-dcm2bids[all]'\n```\n\n## Usage\n\n```python\nfrom pydra.tasks import dcm2bids\n\ntask = dcm2bids.Dcm2Bids(\n dicom_dir=\"/path/to/dicom/dir\",\n output_dir=\"/path/to/bids/dir\",\n config_file=\"/path/to/config/file.json\",\n participant_id=\"sub-01\",\n)\n\nresult = task()\n```\n\nYou may check the following example of a [configuration file][dcm2bids-config-file].\n\n## Development\n\nThis project is managed with [Hatch][hatch]:\n\n```console\npipx install hatch\n```\n\nTo run the test suite:\n\n```console\nhatch run test:no-cov\n```\n\nTo fix linting issues:\n\n```console\nhatch run lint:fix\n```\n\nTo check the documentation:\n\n```console\nhatch run docs:serve --open-browser\n```\n\n## License\n\n`pydra-dcm2bids` is distributed under the terms of the [Apache License, Version 2.0][license].\n\n[pypi-project]: https://pypi.org/project/pydra-dcm2bids\n\n[pypi-version]: https://img.shields.io/pypi/v/pydra-dcm2bids.svg\n\n[pypi-pyversions]: https://img.shields.io/pypi/pyversions/pydra-dcm2bids.svg\n\n[pydra]: https://pydra.readthedocs.io/\n\n[dcm2bids]: https://unfmontreal.github.io/Dcm2Bids/\n\n[bids]: https://bids-specification.readthedocs.io/\n\n[dcm2bids-install]: https://unfmontreal.github.io/Dcm2Bids/docs/get-started/install/\n\n[dcm2bids-config-file]: https://unfmontreal.github.io/Dcm2Bids/docs/how-to/create-config-file/\n\n[hatch]: https://hatch.pypa.io/\n\n[license]: https://spdx.org/licenses/Apache-2.0.html\n",
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