# Pydra Dcm2Niix Task
This repository contains Pydra task interface for the `dcm2niix`
DICOM to NIfTI converter tool (https://github.com/rordenlab/dcm2niix).
Part of this effort is to establish a (mostly) declarative language for describing tasks that
potentially have intricate rules for determining the availability and names from the choice of
inputs.
## Installation
```
pip install /path/to/pydra-dcm2niix/
```
### Installation for developers
```
pip install -e /path/to/pydra-dcm2niix/[dev]
```
## Basic Use
To run the `dcm2niix` task
```
from pydra.tasks.dcm2niix import Dcm2Niix
task = Dcm2Niix(in_dir='/path/to/dicom/dir', out_dir='/path/to/create/nifti/output')
result = task()
```
However, the converter task interface will typically be used as the first step within larger Pydra workflows
```
from pydra import Workflow
from pydra.tasks.dcm2niix import Dcm2Niix
my_workflow = Workflow(name='my_workflow', input_spec=['in_dicom'])
my_workflow.add(
Dcm2Niix(name='converter', in_dir=my_workflow.lzin.in_dicom, out_dir='.'))
my_workflow.add(...)
my_workflow()
```
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"description": "# Pydra Dcm2Niix Task\n\nThis repository contains Pydra task interface for the `dcm2niix`\nDICOM to NIfTI converter tool (https://github.com/rordenlab/dcm2niix).\n\nPart of this effort is to establish a (mostly) declarative language for describing tasks that\npotentially have intricate rules for determining the availability and names from the choice of\ninputs.\n\n## Installation\n```\npip install /path/to/pydra-dcm2niix/\n```\n\n### Installation for developers\n```\npip install -e /path/to/pydra-dcm2niix/[dev]\n```\n\n## Basic Use\n\nTo run the `dcm2niix` task\n\n```\nfrom pydra.tasks.dcm2niix import Dcm2Niix\n\ntask = Dcm2Niix(in_dir='/path/to/dicom/dir', out_dir='/path/to/create/nifti/output')\nresult = task()\n```\n\nHowever, the converter task interface will typically be used as the first step within larger Pydra workflows\n\n```\nfrom pydra import Workflow\nfrom pydra.tasks.dcm2niix import Dcm2Niix\n\nmy_workflow = Workflow(name='my_workflow', input_spec=['in_dicom'])\n\nmy_workflow.add(\n Dcm2Niix(name='converter', in_dir=my_workflow.lzin.in_dicom, out_dir='.'))\nmy_workflow.add(...)\n\nmy_workflow()\n```\n",
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