Metadata-Version: 2.4
Name: pydra-tasks-dcm2niix
Version: 1.3.1
Summary: pydra-tasks-dcm2niix contains Pydra task specifications for the Dcm2niix converter
Author-email: "Thomas G. Close" <tom.g.close@gmail.com>
Maintainer-email: "Thomas G. Close" <tom.g.close@gmail.com>
License:    Copyright 2021 Nipype developers
        
           Licensed under the Apache License, Version 2.0 (the "License");
           you may not use this file except in compliance with the License.
           You may obtain a copy of the License at
        
               http://www.apache.org/licenses/LICENSE-2.0
        
           Unless required by applicable law or agreed to in writing, software
           distributed under the License is distributed on an "AS IS" BASIS,
           WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
           See the License for the specific language governing permissions and
           limitations under the License.
License-File: LICENSE
Keywords: pydra
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering
Requires-Python: >=3.11
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Requires-Dist: pydra>=1.0a
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Description-Content-Type: text/markdown

# 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()
```
