diff --git a/fmriprep/workflows/bold/fit.py b/fmriprep/workflows/bold/fit.py
index ed752492b..319ce24a3 100644
--- a/fmriprep/workflows/bold/fit.py
+++ b/fmriprep/workflows/bold/fit.py
@@ -397,6 +397,8 @@ def init_bold_fit_wf(
         # fmt:off
         workflow.connect([
             (inputnode, bold_reg_wf, [
+                ("t1w_preproc", "inputnode.t1w_preproc"),
+                ("t1w_mask", "inputnode.t1w_mask"),
                 ("t1w_dseg", "inputnode.t1w_dseg"),
                 # Undefined if --fs-no-reconall, but this is safe
                 ("subjects_dir", "inputnode.subjects_dir"),
diff --git a/fmriprep/workflows/bold/registration.py b/fmriprep/workflows/bold/registration.py
index c643bc7cf..7f4c9e57a 100644
--- a/fmriprep/workflows/bold/registration.py
+++ b/fmriprep/workflows/bold/registration.py
@@ -149,7 +149,8 @@ def init_bold_reg_wf(
         niu.IdentityInterface(
             fields=[
                 'ref_bold_brain',
-                't1w_brain',
+                't1w_preproc',
+                't1w_mask',
                 't1w_dseg',
                 'subjects_dir',
                 'subject_id',
@@ -186,8 +187,10 @@ def init_bold_reg_wf(
             ('fsnative2t1w_xfm', 'inputnode.fsnative2t1w_xfm'),
             ('subjects_dir', 'inputnode.subjects_dir'),
             ('subject_id', 'inputnode.subject_id'),
+            ('t1w_preproc', 'inputnode.t1w_brain'),
+            ('t1w_mask', 'inputnode.t1w_mask'),
             ('t1w_dseg', 'inputnode.t1w_dseg'),
-            ('t1w_brain', 'inputnode.t1w_brain')]),
+        ]),
         (bbr_wf, outputnode, [('outputnode.itk_bold_to_t1', 'itk_bold_to_t1'),
                               ('outputnode.itk_t1_to_bold', 'itk_t1_to_bold'),
                               ('outputnode.fallback', 'fallback')]),
@@ -526,13 +529,14 @@ def init_bbreg_wf(
         niu.IdentityInterface(
             [
                 'in_file',
-                'fsnative2t1w_xfm',
+                'fsnative2t1w_xfm',  # BBRegister
                 'subjects_dir',
-                'subject_id',  # BBRegister
+                'subject_id',
+                't1w_preproc',  # FLIRT BBR
+                't1w_mask',
                 't1w_dseg',
-                't1w_brain',
             ]
-        ),  # FLIRT BBR
+        ),
         name='inputnode',
     )
     outputnode = pe.Node(
@@ -736,6 +740,7 @@ def init_fsl_bbr_wf(
     from niworkflows.engine.workflows import LiterateWorkflow as Workflow
     from niworkflows.interfaces.freesurfer import PatchedLTAConvert as LTAConvert
     from niworkflows.interfaces.freesurfer import PatchedMRICoregRPT as MRICoregRPT
+    from niworkflows.interfaces.nibabel import ApplyMask
     from niworkflows.interfaces.reportlets.registration import FLIRTRPT
     from niworkflows.utils.images import dseg_label as _dseg_label
 
@@ -757,13 +762,14 @@ def init_fsl_bbr_wf(
         niu.IdentityInterface(
             [
                 'in_file',
-                'fsnative2t1w_xfm',
+                'fsnative2t1w_xfm',  # BBRegister
                 'subjects_dir',
-                'subject_id',  # BBRegister
+                'subject_id',
+                't1w_preproc',  # FLIRT BBR
+                't1w_mask',
                 't1w_dseg',
-                't1w_brain',
             ]
-        ),  # FLIRT BBR
+        ),
         name='inputnode',
     )
     outputnode = pe.Node(
@@ -780,6 +786,9 @@ def init_fsl_bbr_wf(
     if bold2t1w_init == "header":
         raise NotImplementedError("Header-based registration initialization not supported for FSL")
 
+    # Mask T1w_preproc with T1w_mask to make T1w_brain
+    mask_t1w_brain = pe.Node(ApplyMask(), name='mask_t1w_brain')
+
     mri_coreg = pe.Node(
         MRICoregRPT(
             dof=bold2t1w_dof, sep=[4], ftol=0.0001, linmintol=0.01, generate_report=not use_bbr
@@ -809,12 +818,14 @@ def init_fsl_bbr_wf(
     )
     # fmt:off
     workflow.connect([
-        (inputnode, mri_coreg, [('in_file', 'source_file'),
-                                ('t1w_brain', 'reference_file')]),
-        (inputnode, fsl2itk_fwd, [('t1w_brain', 'reference_file'),
-                                  ('in_file', 'source_file')]),
-        (inputnode, fsl2itk_inv, [('in_file', 'reference_file'),
-                                  ('t1w_brain', 'source_file')]),
+        (inputnode, mask_t1w_brain, [('t1w_preproc', 'in_file'),
+                                     ('t1w_mask', 'in_mask')]),
+        (inputnode, mri_coreg, [('in_file', 'source_file')]),
+        (inputnode, fsl2itk_fwd, [('in_file', 'source_file')]),
+        (inputnode, fsl2itk_inv, [('in_file', 'reference_file')]),
+        (mask_t1w_brain, mri_coreg, [('out_file', 'reference_file')]),
+        (mask_t1w_brain, fsl2itk_fwd, [('out_file', 'reference_file')]),
+        (mask_t1w_brain, fsl2itk_inv, [('out_file', 'source_file')]),
         (mri_coreg, lta_to_fsl, [('out_lta_file', 'in_lta')]),
         (invt_bbr, fsl2itk_inv, [('out_file', 'transform_file')]),
         (fsl2itk_fwd, outputnode, [('itk_transform', 'itk_bold_to_t1')]),