diff --git a/fmriprep/workflows/bold/fit.py b/fmriprep/workflows/bold/fit.py
index 1d8e2b937..183bbb300 100644
--- a/fmriprep/workflows/bold/fit.py
+++ b/fmriprep/workflows/bold/fit.py
@@ -28,7 +28,11 @@
 import nibabel as nb
 from nipype.interfaces import utility as niu
 from nipype.pipeline import engine as pe
-from niworkflows.func.util import init_enhance_and_skullstrip_bold_wf, init_skullstrip_bold_wf
+from niworkflows.func.util import (
+    init_bold_premask_wf,
+    init_enhance_and_skullstrip_bold_wf,
+    init_skullstrip_bold_wf,
+)
 from niworkflows.interfaces.header import ValidateImage
 from niworkflows.interfaces.nitransforms import ConcatenateXFMs
 from niworkflows.interfaces.utility import KeySelect
@@ -549,16 +553,28 @@ def init_bold_fit_wf(
     if not coreg_boldref:
         config.loggers.workflow.info('Stage 4: Adding coregistration boldref workflow')
 
-        # If sbref files are available, add them to the list of sources
-        if sbref_files and nb.load(sbref_files[0]).ndim > 3:
-            raw_sbref_wf = init_raw_boldref_wf(
-                name='raw_sbref_wf',
-                bold_file=sbref_files[0],
-                multiecho=len(sbref_files) > 1,
-            )
-            workflow.connect(raw_sbref_wf, 'outputnode.boldref', fmapref_buffer, 'sbref_files')
+        enhance_and_skullstrip_bold_wf = init_enhance_and_skullstrip_bold_wf(
+            omp_nthreads=omp_nthreads,
+            pre_mask=bool(sbref_files),
+        )
+
+        if sbref_files:
+            if nb.load(sbref_files[0]).ndim > 3:  # multivolume
+                raw_sbref_wf = init_raw_boldref_wf(
+                    name='raw_sbref_wf',
+                    bold_file=sbref_files[0],
+                    multiecho=len(sbref_files) > 1,
+                )
+                workflow.connect(raw_sbref_wf, 'outputnode.boldref', fmapref_buffer, 'sbref_files')
+
+            bold_premask_wf = init_bold_premask_wf(omp_nthreads=omp_nthreads)
+            workflow.connect([
+                (hmcref_buffer, bold_premask_wf, [('boldref', 'inputnode.in_file')]),
+                (bold_premask_wf, enhance_and_skullstrip_bold_wf, [
+                    ('outputnode.mask_file', 'inputnode.pre_mask'),
+                ]),
+            ])  # fmt:skip
 
-        enhance_boldref_wf = init_enhance_and_skullstrip_bold_wf(omp_nthreads=omp_nthreads)
         coreg_ref_source_files = pe.Node(
             niu.Merge(3), name='coreg_ref_source_files', run_without_submitting=True
         )
@@ -578,7 +594,7 @@ def init_bold_fit_wf(
         )
 
         workflow.connect([
-            (fmapref_buffer, enhance_boldref_wf, [('out', 'inputnode.in_file')]),
+            (fmapref_buffer, enhance_and_skullstrip_bold_wf, [('out', 'inputnode.in_file')]),
             (fmapref_buffer, coreg_ref_source_files, [('out', 'in1')]),
             (coreg_ref_source_files, ds_coreg_boldref_wf, [('out', 'inputnode.source_files')]),
             (ds_coreg_boldref_wf, regref_buffer, [('outputnode.boldref', 'boldref')]),
@@ -608,7 +624,7 @@ def init_bold_fit_wf(
 
             workflow.connect([
                 (fmapref_buffer, unwarp_boldref, [('out', 'ref_file')]),
-                (enhance_boldref_wf, unwarp_boldref, [
+                (enhance_and_skullstrip_bold_wf, unwarp_boldref, [
                     ('outputnode.bias_corrected_file', 'in_file'),
                 ]),
                 (boldref_fmap, unwarp_boldref, [('out_file', 'fieldmap')]),
@@ -631,17 +647,17 @@ def init_bold_fit_wf(
 
             if not boldref2fmap_xform:
                 workflow.connect([
-                    (enhance_boldref_wf, fmapreg_wf, [
+                    (enhance_and_skullstrip_bold_wf, fmapreg_wf, [
                         ('outputnode.bias_corrected_file', 'inputnode.target_ref'),
                         ('outputnode.mask_file', 'inputnode.target_mask'),
                     ]),
                 ])  # fmt:skip
         else:
             workflow.connect([
-                (enhance_boldref_wf, ds_coreg_boldref_wf, [
+                (enhance_and_skullstrip_bold_wf, ds_coreg_boldref_wf, [
                     ('outputnode.bias_corrected_file', 'inputnode.boldref'),
                 ]),
-                (enhance_boldref_wf, ds_boldmask_wf, [
+                (enhance_and_skullstrip_bold_wf, ds_boldmask_wf, [
                     ('outputnode.mask_file', 'inputnode.boldmask'),
                 ]),
             ])  # fmt:skip
diff --git a/pixi.lock b/pixi.lock
index 778717d58..515bc3bda 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -303,7 +303,7 @@ environments:
       - pypi: https://files.pythonhosted.org/packages/91/53/c5ad0140e2e4c4d92ae45558587e26b2ebc62e39eafa30b74cb052d9375b/nipype-1.10.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/4e/23/f87d9328c96e0107fed479ec564ce645b033ae0d6cedad2672bddeb0e065/nireports-25.3.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/fa/71/e399826fda4c9f41bd3b895c7d5612d4eae76269519ea923ece9f798f79f/nitransforms-25.1.0-py3-none-any.whl
-      - pypi: https://files.pythonhosted.org/packages/75/ef/021d66cd659183dcfd818cc571ec63275ad93eb9a5e319e3b86e44305aa4/niworkflows-1.14.2-py3-none-any.whl
+      - pypi: git+https://github.com/nipreps/niworkflows.git?rev=refs%2Fpull%2F1001%2Fhead#9c3c22d51787f2dec850db60b24c8ec677c84302
       - pypi: https://files.pythonhosted.org/packages/d6/5b/545e9267a1cc080c8a1be2746113a063e34bcdd0f5173fd665a5c13cb234/num2words-0.5.14-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/7f/96/d6d25a4c307d6645f4a9b91d620c0151c544ad38b5e371313a87d2761004/nvidia_ml_py-13.580.82-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/b8/db/14bafcb4af2139e046d03fd00dea7873e48eafe18b7d2797e73d6681f210/prometheus_client-0.23.1-py3-none-any.whl
@@ -679,7 +679,7 @@ environments:
       - pypi: https://files.pythonhosted.org/packages/91/53/c5ad0140e2e4c4d92ae45558587e26b2ebc62e39eafa30b74cb052d9375b/nipype-1.10.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/4e/23/f87d9328c96e0107fed479ec564ce645b033ae0d6cedad2672bddeb0e065/nireports-25.3.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/fa/71/e399826fda4c9f41bd3b895c7d5612d4eae76269519ea923ece9f798f79f/nitransforms-25.1.0-py3-none-any.whl
-      - pypi: https://files.pythonhosted.org/packages/75/ef/021d66cd659183dcfd818cc571ec63275ad93eb9a5e319e3b86e44305aa4/niworkflows-1.14.2-py3-none-any.whl
+      - pypi: git+https://github.com/nipreps/niworkflows.git?rev=refs%2Fpull%2F1001%2Fhead#9c3c22d51787f2dec850db60b24c8ec677c84302
       - pypi: https://files.pythonhosted.org/packages/d6/5b/545e9267a1cc080c8a1be2746113a063e34bcdd0f5173fd665a5c13cb234/num2words-0.5.14-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/7f/96/d6d25a4c307d6645f4a9b91d620c0151c544ad38b5e371313a87d2761004/nvidia_ml_py-13.580.82-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/a8/7a/8d6fe30d424329ced46a738faaea4150efb8eee656599b88a791cf7ad07e/osfclient-0.0.5-py2.py3-none-any.whl
@@ -1043,7 +1043,7 @@ environments:
       - pypi: https://files.pythonhosted.org/packages/91/53/c5ad0140e2e4c4d92ae45558587e26b2ebc62e39eafa30b74cb052d9375b/nipype-1.10.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/4e/23/f87d9328c96e0107fed479ec564ce645b033ae0d6cedad2672bddeb0e065/nireports-25.3.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/fa/71/e399826fda4c9f41bd3b895c7d5612d4eae76269519ea923ece9f798f79f/nitransforms-25.1.0-py3-none-any.whl
-      - pypi: https://files.pythonhosted.org/packages/75/ef/021d66cd659183dcfd818cc571ec63275ad93eb9a5e319e3b86e44305aa4/niworkflows-1.14.2-py3-none-any.whl
+      - pypi: git+https://github.com/nipreps/niworkflows.git?rev=refs%2Fpull%2F1001%2Fhead#9c3c22d51787f2dec850db60b24c8ec677c84302
       - pypi: https://files.pythonhosted.org/packages/d6/5b/545e9267a1cc080c8a1be2746113a063e34bcdd0f5173fd665a5c13cb234/num2words-0.5.14-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/7f/96/d6d25a4c307d6645f4a9b91d620c0151c544ad38b5e371313a87d2761004/nvidia_ml_py-13.580.82-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/54/20/4d324d65cc6d9205fabedc306948156824eb9f0ee1633355a8f7ec5c66bf/pluggy-1.6.0-py3-none-any.whl
@@ -2132,8 +2132,8 @@ packages:
   requires_python: '>=3.9'
 - pypi: ./
   name: fmriprep
-  version: 25.3.0.dev11+gdc6509538
-  sha256: eb5e8869ff7f7c3c3454e11c4248ea8fe432f10ad9e70d2cc2240e0c29e2209a
+  version: 25.3.0.dev27+ge25dd8080
+  sha256: d4557fff8cec13691a541bf00ffc033bb6f66ccb575a1c4a7026b711aa6c9911
   requires_dist:
   - acres>=0.2.0
   - apscheduler>=3.10
@@ -2144,7 +2144,7 @@ packages:
   - nireports>=24.1.0
   - nitime>=0.9
   - nitransforms>=25.0.1
-  - niworkflows>=1.14.2
+  - niworkflows @ git+https://github.com/nipreps/niworkflows.git@refs/pull/1001/head
   - numpy>=2.0
   - packaging>=24
   - pandas>=2.2
@@ -2203,8 +2203,8 @@ packages:
   editable: true
 - pypi: ./
   name: fmriprep
-  version: 25.3.0.dev11+gdc6509538
-  sha256: eb5e8869ff7f7c3c3454e11c4248ea8fe432f10ad9e70d2cc2240e0c29e2209a
+  version: 25.3.0.dev27+ge25dd8080
+  sha256: d4557fff8cec13691a541bf00ffc033bb6f66ccb575a1c4a7026b711aa6c9911
   requires_dist:
   - acres>=0.2.0
   - apscheduler>=3.10
@@ -2215,7 +2215,7 @@ packages:
   - nireports>=24.1.0
   - nitime>=0.9
   - nitransforms>=25.0.1
-  - niworkflows>=1.14.2
+  - niworkflows @ git+https://github.com/nipreps/niworkflows.git@refs/pull/1001/head
   - numpy>=2.0
   - packaging>=24
   - pandas>=2.2
@@ -5031,42 +5031,41 @@ packages:
   - nitransforms[test] ; extra == 'tests'
   - nitransforms[test] ; extra == 'all'
   requires_python: '>=3.10'
-- pypi: https://files.pythonhosted.org/packages/75/ef/021d66cd659183dcfd818cc571ec63275ad93eb9a5e319e3b86e44305aa4/niworkflows-1.14.2-py3-none-any.whl
+- pypi: git+https://github.com/nipreps/niworkflows.git?rev=refs%2Fpull%2F1001%2Fhead#9c3c22d51787f2dec850db60b24c8ec677c84302
   name: niworkflows
-  version: 1.14.2
-  sha256: b8871304510372067caf3774017448af70de381a5f2f6337ffb13069b2eeca1c
+  version: 1.15.0.dev34+g9c3c22d51
   requires_dist:
-  - acres
-  - attrs>=20.1
+  - acres>=0.5
+  - attrs>=23.1
   - jinja2>=3
-  - looseversion
-  - matplotlib>=3.5
-  - nibabel>=3.0
-  - nilearn>=0.8
-  - nipype>=1.8.5
-  - nitransforms>=22.0.0
-  - numpy>=1.20
+  - looseversion>=1.3
+  - matplotlib>=3.7
+  - nibabel>=5.0
+  - nilearn>=0.10
+  - nipype>=1.9.1
+  - nitransforms>=23.0.0
+  - numpy>=1.24
   - packaging
-  - pandas>=1.2
-  - pybids>=0.15.1
-  - pyyaml>=5.4
-  - scikit-image>=0.18
-  - scipy>=1.8
-  - seaborn>=0.11
+  - pandas>=2.0
+  - pybids>=0.16
+  - pyyaml>=6.0
+  - scikit-image>=0.20
+  - scipy>=1.10
+  - seaborn>=0.13
   - svgutils>=0.3.4
   - templateflow>=23.1
   - transforms3d>=0.4
-  - coverage[toml]>=5.2.1 ; extra == 'all'
+  - coverage[toml]>=7 ; extra == 'all'
   - flake8>=3.7.0 ; extra == 'all'
   - furo ; extra == 'all'
   - pydot>=1.2.3 ; extra == 'all'
   - pydotplus ; extra == 'all'
   - pyntcloud ; extra == 'all'
-  - pytest-cov>=2.11 ; extra == 'all'
+  - pytest-cov>=7 ; extra == 'all'
   - pytest-env ; extra == 'all'
-  - pytest-xdist>=2.5 ; extra == 'all'
+  - pytest-xdist>=3.8 ; extra == 'all'
   - pytest-xvfb>=2 ; extra == 'all'
-  - pytest>=6 ; extra == 'all'
+  - pytest>=8 ; extra == 'all'
   - sphinx ; extra == 'all'
   - sphinxcontrib-apidoc ; extra == 'all'
   - sphinxcontrib-napoleon ; extra == 'all'
@@ -5084,13 +5083,13 @@ packages:
   - sphinxcontrib-napoleon ; extra == 'docs'
   - pyntcloud ; extra == 'pointclouds'
   - flake8>=3.7.0 ; extra == 'style'
-  - coverage[toml]>=5.2.1 ; extra == 'tests'
-  - pytest-cov>=2.11 ; extra == 'tests'
+  - coverage[toml]>=7 ; extra == 'tests'
+  - pytest-cov>=7 ; extra == 'tests'
   - pytest-env ; extra == 'tests'
-  - pytest-xdist>=2.5 ; extra == 'tests'
+  - pytest-xdist>=3.8 ; extra == 'tests'
   - pytest-xvfb>=2 ; extra == 'tests'
-  - pytest>=6 ; extra == 'tests'
-  requires_python: '>=3.9'
+  - pytest>=8 ; extra == 'tests'
+  requires_python: '>=3.10'
 - conda: https://conda.anaconda.org/conda-forge/linux-64/nodejs-20.19.5-hf7ee748_0.conda
   sha256: f4a33f44d54552ae976c7cec0b915a625b4a4c910faea4338af750539ae69db6
   md5: 2cbd9a01ac939d85f137ee44c64fb705
diff --git a/pyproject.toml b/pyproject.toml
index a27ab211f..a060d7cd9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -27,7 +27,7 @@ dependencies = [
     "nireports >= 24.1.0",
     "nitime >= 0.9",
     "nitransforms >= 25.0.1",
-    "niworkflows >= 1.14.2",
+    "niworkflows @ git+https://github.com/nipreps/niworkflows.git@refs/pull/1001/head",
     "numpy >= 2.0",
     "packaging >= 24",
     "pandas >= 2.2",