diff --git a/fmriprep/workflows/bold/base.py b/fmriprep/workflows/bold/base.py
index 6a3899ef2..1e1acb870 100644
--- a/fmriprep/workflows/bold/base.py
+++ b/fmriprep/workflows/bold/base.py
@@ -294,7 +294,7 @@ def init_func_preproc_wf(bold_file):
     ])
 
     # Generate a tentative boldref
-    bold_reference_wf = init_bold_reference_wf(omp_nthreads=omp_nthreads)
+    bold_reference_wf = init_bold_reference_wf(omp_nthreads=omp_nthreads, brainmask_thresh=0.85)
     bold_reference_wf.inputs.inputnode.dummy_scans = config.workflow.dummy_scans
     if sbref_file is not None:
         workflow.connect([
diff --git a/fmriprep/workflows/bold/registration.py b/fmriprep/workflows/bold/registration.py
index d972ca47d..8433cca55 100644
--- a/fmriprep/workflows/bold/registration.py
+++ b/fmriprep/workflows/bold/registration.py
@@ -325,7 +325,7 @@ def init_bold_t1_trans_wf(freesurfer, mem_gb, omp_nthreads, multiecho=False, use
     merge = pe.Node(Merge(compress=use_compression), name='merge', mem_gb=mem_gb)
 
     # Generate a reference on the target T1w space
-    gen_final_ref = init_bold_reference_wf(omp_nthreads, pre_mask=True)
+    gen_final_ref = init_bold_reference_wf(omp_nthreads, pre_mask=True, brainmask_thresh=0.85)
 
     if not multiecho:
         # Merge transforms placing the head motion correction last
diff --git a/fmriprep/workflows/bold/resampling.py b/fmriprep/workflows/bold/resampling.py
index b7a80ca13..8dea62bb0 100644
--- a/fmriprep/workflows/bold/resampling.py
+++ b/fmriprep/workflows/bold/resampling.py
@@ -352,7 +352,7 @@ def init_bold_std_trans_wf(
 
     # Generate a reference on the target standard space
     gen_final_ref = init_bold_reference_wf(
-        omp_nthreads=omp_nthreads, pre_mask=True)
+        omp_nthreads=omp_nthreads, pre_mask=True, brainmask_thresh=0.85)
 
     workflow.connect([
         (iterablesource, split_target, [('std_target', 'in_target')]),
@@ -526,7 +526,7 @@ def init_bold_preproc_trans_wf(mem_gb, omp_nthreads,
                     mem_gb=mem_gb * 3)
 
     # Generate a new BOLD reference
-    bold_reference_wf = init_bold_reference_wf(omp_nthreads=omp_nthreads)
+    bold_reference_wf = init_bold_reference_wf(omp_nthreads=omp_nthreads, brainmask_thresh=0.85)
     bold_reference_wf.__desc__ = None  # Unset description to avoid second appearance
 
     workflow.connect([
diff --git a/setup.cfg b/setup.cfg
index dbfba502c..baf4ac63d 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -27,7 +27,7 @@ install_requires =
     nipype >= 1.4
     nitime
     nitransforms >= 20.0.0rc3,<20.2
-    niworkflows ~= 1.2.3
+    niworkflows @ git+https://github.com/oesteban/niworkflows.git@294a8679d0a1eb3a7536429b7c794fa902f01703
     numpy
     pandas
     psutil >= 5.4