/pydra-dcm2niix

Pydra task interface for Dcm2niix DICOM to NIfTI conversion utility

Primary LanguagePythonOtherNOASSERTION

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()