Merge pull request #296 from effigies/enh/dilate-pre-tedana

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

Author: mgxd

nibabies/workflows/bold/t2s.py

@@ -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__ = """\
@@ -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')]),
     ])