enh: replace the binary mask of MNI152NLin2009cAsym with the new probseg

Closes #476

Author: oesteban

niworkflows/func/util.py

@@ -286,6 +286,7 @@ def init_enhance_and_skullstrip_bold_wf(
     apply_mask = pe.Node(fsl.ApplyMask(), name='apply_mask')
 
     if not pre_mask:
+        from ..interfaces.nibabel import Binarize
         bold_template = get_template(
             'MNI152NLin2009cAsym', resolution=2, desc='fMRIPrep', suffix='boldref')
         brain_mask = get_template(
@@ -316,10 +317,15 @@ def init_enhance_and_skullstrip_bold_wf(
             name='norm',
             n_procs=omp_nthreads)
         norm.inputs.fixed_image = str(bold_template)
-        map_brainmask = pe.Node(
-            ApplyTransforms(interpolation='MultiLabel', float=True, input_image=str(brain_mask)),
+        map_brainmask = pe.Node(ApplyTransforms(
+            interpolation='BSpline',
+            float=True,
+            # Use the higher resolution and probseg for numerical stability in rounding
+            input_image=str(get_template(
+                'MNI152NLin2009cAsym', resolution=1, desc='brain', suffix='probseg'))),
             name='map_brainmask'
         )
+        binarize_mask = pe.Node(Binarize(thresh_low=0.75), name='binarize_mask')
         workflow.connect([
             (inputnode, init_aff, [('in_file', 'moving_image')]),
             (inputnode, map_brainmask, [('in_file', 'reference_image')]),
@@ -328,7 +334,8 @@ def init_enhance_and_skullstrip_bold_wf(
             (norm, map_brainmask, [
                 ('reverse_invert_flags', 'invert_transform_flags'),
                 ('reverse_transforms', 'transforms')]),
-            (map_brainmask, pre_dilate, [('output_image', 'in_file')]),
+            (map_brainmask, binarize_mask, [('output_image', 'in_file')]),
+            (binarize_mask, pre_dilate, [('out_mask', 'in_file')]),
         ])
     else:
         workflow.connect([

setup.cfg

@@ -38,7 +38,7 @@ install_requires =
     seaborn
     svgutils
     transforms3d
-    templateflow >= 0.4.2
+    templateflow >= 0.5.2
 test_requires =
     coverage < 5
     pytest >= 4.4