sdcflows.workflows.outputs module¶

Writing out outputs.

class sdcflows.workflows.outputs.DerivativesDataSink(allowed_entities=None, out_path_base=None, **inputs)[source]¶

Bases: niworkflows.interfaces.bids.DerivativesDataSink

Overload the out_path_base setting.

out_path_base = 'sdcflows'¶

sdcflows.workflows.outputs.init_fmap_derivatives_wf(*, output_dir, bids_fmap_id=None, custom_entities=None, name='fmap_derivatives_wf', write_coeff=False)[source]¶

Set up datasinks to store derivatives in the right location.

Parameters

output_dir (str) – Directory in which to save derivatives
bids_fmap_id (str) – Sets the B0FieldIdentifier metadata into the outputs.
custom_entities (dict) – Define extra entities that will be written out in filenames.
name (str) – Workflow name (default: "fmap_derivatives_wf")
write_coeff (bool) – Build the workflow path to map coefficients into target space.

Inputs

source_files – One or more fieldmap file(s) of the BIDS dataset that will serve for naming reference.
fieldmap – The preprocessed fieldmap, in its original space with Hz units.
fmap_coeff – Field coefficient(s) file(s)
fmap_ref – An anatomical reference (e.g., magnitude file)

sdcflows.workflows.outputs.init_fmap_reports_wf(*, output_dir, fmap_type, bids_fmap_id=None, custom_entities=None, name='fmap_reports_wf')[source]¶

Set up a battery of datasinks to store reports in the right location.

Parameters

fmap_type (str) – The fieldmap estimator type.
output_dir (str) – Directory in which to save derivatives
bids_fmap_id (str) – Sets the B0FieldIdentifier metadata into the outputs.
custom_entities (dict) – Define extra entities that will be written out in filenames.
name (str) – Workflow name (default: "fmap_reports_wf")

Inputs

source_files – One or more fieldmap file(s) of the BIDS dataset that will serve for naming reference.
fieldmap – The preprocessed fieldmap, in its original space with Hz units.
fmap_ref – An anatomical reference (e.g., magnitude file)
fmap_mask – A brain mask in the fieldmap’s space.