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ENH: Dilate BOLD mask by 2 voxels to prevent over-aggressive masking degrading T2* map estimation #296

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Merged
merged 1 commit into from
Jun 8, 2023
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ENH: Dilate BOLD mask by 2 voxels to prevent over-aggressive masking degrading T2* map estimation #296

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8 changes: 6 additions & 2 deletions nibabies/workflows/bold/t2s.py
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Original file line number Diff line number Diff line change
Expand Up @@ -57,6 +57,7 @@ def init_bold_t2s_wf(echo_times, mem_gb, omp_nthreads, name="bold_t2s_wf"):

"""
from niworkflows.engine.workflows import LiterateWorkflow as Workflow
from niworkflows.interfaces.morphology import BinaryDilation

workflow = Workflow(name=name)
workflow.__desc__ = """\
Expand All @@ -76,12 +77,15 @@ def init_bold_t2s_wf(echo_times, mem_gb, omp_nthreads, name="bold_t2s_wf"):

LOGGER.log(25, "Generating T2* map and optimally combined ME-EPI time series.")

dilate_mask = pe.Node(BinaryDilation(radius=2), name='dilate_mask')

t2smap_node = pe.Node(T2SMap(echo_times=list(echo_times)), name="t2smap_node")

# fmt: off
workflow.connect([
(inputnode, t2smap_node, [('bold_file', 'in_files'),
('bold_mask', 'mask_file')]),
(inputnode, dilate_mask, [('bold_mask', 'in_mask')]),
(inputnode, t2smap_node, [('bold_file', 'in_files')]),
(dilate_mask, t2smap_node, [('out_mask', 'mask_file')]),
(t2smap_node, outputnode, [('optimal_comb', 'bold'),
('t2star_map', 't2star_map')]),
])
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