SABRE’s use of the Nipype neuroimaging workflow engine makes it easy to integrate with other pipelines. The following sections describe SABRE’s Python API.
import nipype.pipeline.engine as pe
from sbl.sabre.workflows import TIVExtractionWorkflow
myworkflow = pe.Workflow('MyWorkflow')
# ...
extract = TIVExtractionWorkflow(template_type='T2')
myworkflow.connect(somenode, 'T2_image', extract, 'T2_image')
myworkflow.connect(somenode, 'PD_image', extract, 'PD_image')
myworkflow.connect(somenode, 'TIV_template', extract, 'TIV_template')
myworkflow.connect(somenode, 'TIV_template_mask', extract, 'TIV_template_mask')
# ...
myworkflow.connect(TIV, 'mask_image', datasink, 'TIV_mask')
# ...
myworkflow.run()
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