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.
pip install /path/to/pydra-dcm2niix/
pip install -e /path/to/pydra-dcm2niix/[dev]
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()