diff --git a/.circleci/ds005_partial_fasttrack_outputs.txt b/.circleci/ds005_partial_fasttrack_outputs.txt
index faa1fc7ad..899352a35 100644
--- a/.circleci/ds005_partial_fasttrack_outputs.txt
+++ b/.circleci/ds005_partial_fasttrack_outputs.txt
@@ -61,6 +61,7 @@ sub-01/anat/sub-01_space-MNI152NLin6Asym_label-CSF_desc-preproc_probseg.nii.gz
 sub-01/anat/sub-01_space-MNI152NLin6Asym_label-GM_desc-preproc_probseg.nii.gz
 sub-01/anat/sub-01_space-MNI152NLin6Asym_label-WM_desc-preproc_probseg.nii.gz
 sub-01/fmap
+sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-brain_mask.nii.gz
 sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-coeff_fieldmap.nii.gz
 sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-magnitude_fieldmap.nii.gz
 sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-preproc_fieldmap.json
@@ -76,8 +77,8 @@ sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-hmc_boldref.json
 sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-hmc_boldref.nii.gz
 sub-01/func/sub-01_task-mixedgamblestask_run-02_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
 sub-01/func/sub-01_task-mixedgamblestask_run-02_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
-sub-01/func/sub-01_task-mixedgamblestask_run-02_from-boldref_to-auto00000_mode-image_xfm.json
-sub-01/func/sub-01_task-mixedgamblestask_run-02_from-boldref_to-auto00000_mode-image_xfm.txt
+sub-01/func/sub-01_task-mixedgamblestask_run-02_from-boldref_to-auto00000_mode-image_desc-fmap_xfm.json
+sub-01/func/sub-01_task-mixedgamblestask_run-02_from-boldref_to-auto00000_mode-image_desc-fmap_xfm.txt
 sub-01/func/sub-01_task-mixedgamblestask_run-02_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
 sub-01/func/sub-01_task-mixedgamblestask_run-02_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
 sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-L_space-fsaverage5_bold.func.gii
diff --git a/.circleci/ds005_partial_outputs.txt b/.circleci/ds005_partial_outputs.txt
index 319a04496..ba934e6fd 100644
--- a/.circleci/ds005_partial_outputs.txt
+++ b/.circleci/ds005_partial_outputs.txt
@@ -83,6 +83,7 @@ sub-01/anat/sub-01_space-MNI152NLin6Asym_label-CSF_probseg.nii.gz
 sub-01/anat/sub-01_space-MNI152NLin6Asym_label-GM_probseg.nii.gz
 sub-01/anat/sub-01_space-MNI152NLin6Asym_label-WM_probseg.nii.gz
 sub-01/fmap
+sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-brain_mask.nii.gz
 sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-coeff_fieldmap.nii.gz
 sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-magnitude_fieldmap.nii.gz
 sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-preproc_fieldmap.json
@@ -96,8 +97,8 @@ sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-coreg_boldref.json
 sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-coreg_boldref.nii.gz
 sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-hmc_boldref.json
 sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-hmc_boldref.nii.gz
-sub-01/func/sub-01_task-mixedgamblestask_run-02_from-boldref_to-auto00000_mode-image_xfm.json
-sub-01/func/sub-01_task-mixedgamblestask_run-02_from-boldref_to-auto00000_mode-image_xfm.txt
+sub-01/func/sub-01_task-mixedgamblestask_run-02_from-boldref_to-auto00000_mode-image_desc-fmap_xfm.json
+sub-01/func/sub-01_task-mixedgamblestask_run-02_from-boldref_to-auto00000_mode-image_desc-fmap_xfm.txt
 sub-01/func/sub-01_task-mixedgamblestask_run-02_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
 sub-01/func/sub-01_task-mixedgamblestask_run-02_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
 sub-01/func/sub-01_task-mixedgamblestask_run-02_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
diff --git a/.circleci/ds054_fasttrack_outputs.txt b/.circleci/ds054_fasttrack_outputs.txt
index c9327680f..c806b68e9 100644
--- a/.circleci/ds054_fasttrack_outputs.txt
+++ b/.circleci/ds054_fasttrack_outputs.txt
@@ -18,6 +18,7 @@ sub-100185/anat/sub-100185_space-MNI152NLin2009cAsym_res-2_label-CSF_desc-prepro
 sub-100185/anat/sub-100185_space-MNI152NLin2009cAsym_res-2_label-GM_desc-preproc_probseg.nii.gz
 sub-100185/anat/sub-100185_space-MNI152NLin2009cAsym_res-2_label-WM_desc-preproc_probseg.nii.gz
 sub-100185/fmap
+sub-100185/fmap/sub-100185_fmapid-auto00000_desc-brain_mask.nii.gz
 sub-100185/fmap/sub-100185_fmapid-auto00000_desc-coeff_fieldmap.nii.gz
 sub-100185/fmap/sub-100185_fmapid-auto00000_desc-magnitude_fieldmap.nii.gz
 sub-100185/fmap/sub-100185_fmapid-auto00000_desc-preproc_fieldmap.json
@@ -33,8 +34,8 @@ sub-100185/func/sub-100185_task-machinegame_run-01_desc-hmc_boldref.json
 sub-100185/func/sub-100185_task-machinegame_run-01_desc-hmc_boldref.nii.gz
 sub-100185/func/sub-100185_task-machinegame_run-01_desc-preproc_bold.json
 sub-100185/func/sub-100185_task-machinegame_run-01_desc-preproc_bold.nii.gz
-sub-100185/func/sub-100185_task-machinegame_run-01_from-boldref_to-auto00000_mode-image_xfm.json
-sub-100185/func/sub-100185_task-machinegame_run-01_from-boldref_to-auto00000_mode-image_xfm.txt
+sub-100185/func/sub-100185_task-machinegame_run-01_from-boldref_to-auto00000_mode-image_desc-fmap_xfm.json
+sub-100185/func/sub-100185_task-machinegame_run-01_from-boldref_to-auto00000_mode-image_desc-fmap_xfm.txt
 sub-100185/func/sub-100185_task-machinegame_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
 sub-100185/func/sub-100185_task-machinegame_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
 sub-100185/func/sub-100185_task-machinegame_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
@@ -61,8 +62,8 @@ sub-100185/func/sub-100185_task-machinegame_run-02_desc-hmc_boldref.json
 sub-100185/func/sub-100185_task-machinegame_run-02_desc-hmc_boldref.nii.gz
 sub-100185/func/sub-100185_task-machinegame_run-02_desc-preproc_bold.json
 sub-100185/func/sub-100185_task-machinegame_run-02_desc-preproc_bold.nii.gz
-sub-100185/func/sub-100185_task-machinegame_run-02_from-boldref_to-auto00000_mode-image_xfm.json
-sub-100185/func/sub-100185_task-machinegame_run-02_from-boldref_to-auto00000_mode-image_xfm.txt
+sub-100185/func/sub-100185_task-machinegame_run-02_from-boldref_to-auto00000_mode-image_desc-fmap_xfm.json
+sub-100185/func/sub-100185_task-machinegame_run-02_from-boldref_to-auto00000_mode-image_desc-fmap_xfm.txt
 sub-100185/func/sub-100185_task-machinegame_run-02_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
 sub-100185/func/sub-100185_task-machinegame_run-02_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
 sub-100185/func/sub-100185_task-machinegame_run-02_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
diff --git a/.circleci/ds054_outputs.txt b/.circleci/ds054_outputs.txt
index 1340f33be..f50701f6f 100644
--- a/.circleci/ds054_outputs.txt
+++ b/.circleci/ds054_outputs.txt
@@ -28,6 +28,7 @@ sub-100185/anat/sub-100185_space-MNI152NLin2009cAsym_res-2_label-CSF_probseg.nii
 sub-100185/anat/sub-100185_space-MNI152NLin2009cAsym_res-2_label-GM_probseg.nii.gz
 sub-100185/anat/sub-100185_space-MNI152NLin2009cAsym_res-2_label-WM_probseg.nii.gz
 sub-100185/fmap
+sub-100185/fmap/sub-100185_fmapid-auto00000_desc-brain_mask.nii.gz
 sub-100185/fmap/sub-100185_fmapid-auto00000_desc-coeff_fieldmap.nii.gz
 sub-100185/fmap/sub-100185_fmapid-auto00000_desc-magnitude_fieldmap.nii.gz
 sub-100185/fmap/sub-100185_fmapid-auto00000_desc-preproc_fieldmap.json
@@ -43,8 +44,8 @@ sub-100185/func/sub-100185_task-machinegame_run-01_desc-hmc_boldref.json
 sub-100185/func/sub-100185_task-machinegame_run-01_desc-hmc_boldref.nii.gz
 sub-100185/func/sub-100185_task-machinegame_run-01_desc-preproc_bold.json
 sub-100185/func/sub-100185_task-machinegame_run-01_desc-preproc_bold.nii.gz
-sub-100185/func/sub-100185_task-machinegame_run-01_from-boldref_to-auto00000_mode-image_xfm.json
-sub-100185/func/sub-100185_task-machinegame_run-01_from-boldref_to-auto00000_mode-image_xfm.txt
+sub-100185/func/sub-100185_task-machinegame_run-01_from-boldref_to-auto00000_mode-image_desc-fmap_xfm.json
+sub-100185/func/sub-100185_task-machinegame_run-01_from-boldref_to-auto00000_mode-image_desc-fmap_xfm.txt
 sub-100185/func/sub-100185_task-machinegame_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
 sub-100185/func/sub-100185_task-machinegame_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
 sub-100185/func/sub-100185_task-machinegame_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
@@ -71,8 +72,8 @@ sub-100185/func/sub-100185_task-machinegame_run-02_desc-hmc_boldref.json
 sub-100185/func/sub-100185_task-machinegame_run-02_desc-hmc_boldref.nii.gz
 sub-100185/func/sub-100185_task-machinegame_run-02_desc-preproc_bold.json
 sub-100185/func/sub-100185_task-machinegame_run-02_desc-preproc_bold.nii.gz
-sub-100185/func/sub-100185_task-machinegame_run-02_from-boldref_to-auto00000_mode-image_xfm.json
-sub-100185/func/sub-100185_task-machinegame_run-02_from-boldref_to-auto00000_mode-image_xfm.txt
+sub-100185/func/sub-100185_task-machinegame_run-02_from-boldref_to-auto00000_mode-image_desc-fmap_xfm.json
+sub-100185/func/sub-100185_task-machinegame_run-02_from-boldref_to-auto00000_mode-image_desc-fmap_xfm.txt
 sub-100185/func/sub-100185_task-machinegame_run-02_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
 sub-100185/func/sub-100185_task-machinegame_run-02_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
 sub-100185/func/sub-100185_task-machinegame_run-02_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
diff --git a/.circleci/ds210_fasttrack_outputs.txt b/.circleci/ds210_fasttrack_outputs.txt
index 2bc78e426..e5361b1f8 100644
--- a/.circleci/ds210_fasttrack_outputs.txt
+++ b/.circleci/ds210_fasttrack_outputs.txt
@@ -17,6 +17,7 @@ sub-02/anat/sub-02_space-MNI152NLin2009cAsym_label-CSF_desc-preproc_probseg.nii.
 sub-02/anat/sub-02_space-MNI152NLin2009cAsym_label-GM_desc-preproc_probseg.nii.gz
 sub-02/anat/sub-02_space-MNI152NLin2009cAsym_label-WM_desc-preproc_probseg.nii.gz
 sub-02/fmap
+sub-02/fmap/sub-02_run-01_fmapid-auto00000_desc-brain_mask.nii.gz
 sub-02/fmap/sub-02_run-01_fmapid-auto00000_desc-coeff_fieldmap.nii.gz
 sub-02/fmap/sub-02_run-01_fmapid-auto00000_desc-magnitude_fieldmap.nii.gz
 sub-02/fmap/sub-02_run-01_fmapid-auto00000_desc-preproc_fieldmap.json
@@ -36,8 +37,8 @@ sub-02/func/sub-02_task-cuedSGT_run-01_echo-2_desc-preproc_bold.json
 sub-02/func/sub-02_task-cuedSGT_run-01_echo-2_desc-preproc_bold.nii.gz
 sub-02/func/sub-02_task-cuedSGT_run-01_echo-3_desc-preproc_bold.json
 sub-02/func/sub-02_task-cuedSGT_run-01_echo-3_desc-preproc_bold.nii.gz
-sub-02/func/sub-02_task-cuedSGT_run-01_from-boldref_to-auto00000_mode-image_xfm.json
-sub-02/func/sub-02_task-cuedSGT_run-01_from-boldref_to-auto00000_mode-image_xfm.txt
+sub-02/func/sub-02_task-cuedSGT_run-01_from-boldref_to-auto00000_mode-image_desc-fmap_xfm.json
+sub-02/func/sub-02_task-cuedSGT_run-01_from-boldref_to-auto00000_mode-image_desc-fmap_xfm.txt
 sub-02/func/sub-02_task-cuedSGT_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
 sub-02/func/sub-02_task-cuedSGT_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
 sub-02/func/sub-02_task-cuedSGT_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
diff --git a/.circleci/ds210_outputs.txt b/.circleci/ds210_outputs.txt
index b1fc5226e..b0439969b 100644
--- a/.circleci/ds210_outputs.txt
+++ b/.circleci/ds210_outputs.txt
@@ -27,6 +27,7 @@ sub-02/anat/sub-02_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz
 sub-02/anat/sub-02_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz
 sub-02/anat/sub-02_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz
 sub-02/fmap
+sub-02/fmap/sub-02_run-01_fmapid-auto00000_desc-brain_mask.nii.gz
 sub-02/fmap/sub-02_run-01_fmapid-auto00000_desc-coeff_fieldmap.nii.gz
 sub-02/fmap/sub-02_run-01_fmapid-auto00000_desc-magnitude_fieldmap.nii.gz
 sub-02/fmap/sub-02_run-01_fmapid-auto00000_desc-preproc_fieldmap.json
@@ -46,8 +47,8 @@ sub-02/func/sub-02_task-cuedSGT_run-01_echo-2_desc-preproc_bold.json
 sub-02/func/sub-02_task-cuedSGT_run-01_echo-2_desc-preproc_bold.nii.gz
 sub-02/func/sub-02_task-cuedSGT_run-01_echo-3_desc-preproc_bold.json
 sub-02/func/sub-02_task-cuedSGT_run-01_echo-3_desc-preproc_bold.nii.gz
-sub-02/func/sub-02_task-cuedSGT_run-01_from-boldref_to-auto00000_mode-image_xfm.json
-sub-02/func/sub-02_task-cuedSGT_run-01_from-boldref_to-auto00000_mode-image_xfm.txt
+sub-02/func/sub-02_task-cuedSGT_run-01_from-boldref_to-auto00000_mode-image_desc-fmap_xfm.json
+sub-02/func/sub-02_task-cuedSGT_run-01_from-boldref_to-auto00000_mode-image_desc-fmap_xfm.txt
 sub-02/func/sub-02_task-cuedSGT_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
 sub-02/func/sub-02_task-cuedSGT_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
 sub-02/func/sub-02_task-cuedSGT_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
diff --git a/fmriprep/workflows/bold/base.py b/fmriprep/workflows/bold/base.py
index bc7586416..d1f1733b7 100644
--- a/fmriprep/workflows/bold/base.py
+++ b/fmriprep/workflows/bold/base.py
@@ -314,6 +314,7 @@ def init_bold_wf(
 
     if boldref_out or echos_out:
         ds_bold_native_wf = init_ds_bold_native_wf(
+            source_file=bold_series,
             bids_root=str(config.execution.bids_dir),
             output_dir=fmriprep_dir,
             bold_output=boldref_out,
@@ -372,9 +373,14 @@ def init_bold_wf(
         for node in workflow.list_node_names():
             if node.split('.')[-1].startswith('ds_report'):
                 workflow.get_node(node).inputs.base_directory = fmriprep_dir
-                workflow.get_node(node).inputs.source_file = bold_file
         return workflow
 
+    # Pass along BOLD reference as a source file for provenance
+    merge_bold_sources = pe.Node(
+        niu.Merge(2), name='merge_bold_sources', run_without_submitting=True
+    )
+    merge_bold_sources.inputs.in1 = bold_series
+
     # Resample to anatomical space
     bold_anat_wf = init_bold_volumetric_resample_wf(
         metadata=all_metadata[0],
@@ -404,18 +410,19 @@ def init_bold_wf(
             ('outputnode.bold_minimal', 'inputnode.bold_file'),
             ('outputnode.motion_xfm', 'inputnode.motion_xfm'),
         ]),
+        (bold_fit_wf, merge_bold_sources, [('outputnode.coreg_boldref', 'in2')]),
     ])  # fmt:skip
 
     # Full derivatives, including resampled BOLD series
     if nonstd_spaces.intersection(('anat', 'T1w')):
         ds_bold_t1_wf = init_ds_volumes_wf(
+            source_file=bold_file,
             bids_root=str(config.execution.bids_dir),
             output_dir=fmriprep_dir,
             multiecho=multiecho,
             metadata=all_metadata[0],
             name='ds_bold_t1_wf',
         )
-        ds_bold_t1_wf.inputs.inputnode.source_files = bold_series
         ds_bold_t1_wf.inputs.inputnode.space = 'T1w'
 
         workflow.connect([
@@ -431,6 +438,7 @@ def init_bold_wf(
                 ('outputnode.bold_file', 'inputnode.bold'),
                 ('outputnode.resampling_reference', 'inputnode.ref_file'),
             ]),
+            (merge_bold_sources, ds_bold_t1_wf, [('out', 'inputnode.source_files')]),
         ])  # fmt:skip
 
     if spaces.cached.get_spaces(nonstandard=False, dim=(3,)):
@@ -446,13 +454,13 @@ def init_bold_wf(
             name='bold_std_wf',
         )
         ds_bold_std_wf = init_ds_volumes_wf(
+            source_file=bold_file,
             bids_root=str(config.execution.bids_dir),
             output_dir=fmriprep_dir,
             multiecho=multiecho,
             metadata=all_metadata[0],
             name='ds_bold_std_wf',
         )
-        ds_bold_std_wf.inputs.inputnode.source_files = bold_series
 
         workflow.connect([
             (inputnode, bold_std_wf, [
@@ -492,6 +500,7 @@ def init_bold_wf(
                 ('outputnode.bold_file', 'inputnode.bold'),
                 ('outputnode.resampling_reference', 'inputnode.ref_file'),
             ]),
+            (merge_bold_sources, ds_bold_std_wf, [('out', 'inputnode.source_files')]),
         ])  # fmt:skip
 
     if config.workflow.run_reconall and freesurfer_spaces:
diff --git a/fmriprep/workflows/bold/fit.py b/fmriprep/workflows/bold/fit.py
index 4017aa2bf..0586cde92 100644
--- a/fmriprep/workflows/bold/fit.py
+++ b/fmriprep/workflows/bold/fit.py
@@ -348,6 +348,7 @@ def init_bold_fit_wf(
         )
 
     func_fit_reports_wf = init_func_fit_reports_wf(
+        source_file=bold_file,
         sdc_correction=fieldmap_id is not None,
         freesurfer=config.workflow.run_reconall,
         output_dir=config.execution.fmriprep_dir,
@@ -368,7 +369,6 @@ def init_bold_fit_wf(
             ('hmc_xforms', 'motion_xfm'),
         ]),
         (inputnode, func_fit_reports_wf, [
-            ('bold_file', 'inputnode.source_file'),
             ('t1w_preproc', 'inputnode.t1w_preproc'),
             # May not need all of these
             ('t1w_mask', 'inputnode.t1w_mask'),
@@ -399,6 +399,7 @@ def init_bold_fit_wf(
         hmc_boldref_wf.inputs.inputnode.dummy_scans = config.workflow.dummy_scans
 
         ds_hmc_boldref_wf = init_ds_boldref_wf(
+            source_file=bold_file,
             bids_root=layout.root,
             output_dir=config.execution.fmriprep_dir,
             desc='hmc',
@@ -407,12 +408,12 @@ def init_bold_fit_wf(
         ds_hmc_boldref_wf.inputs.inputnode.source_files = [bold_file]
 
         workflow.connect([
+            (hmc_boldref_wf, ds_hmc_boldref_wf, [('outputnode.boldref', 'inputnode.boldref')]),
+            (ds_hmc_boldref_wf, hmcref_buffer, [('outputnode.boldref', 'boldref')]),
             (hmc_boldref_wf, hmcref_buffer, [
                 ('outputnode.bold_file', 'bold_file'),
-                ('outputnode.boldref', 'boldref'),
                 ('outputnode.skip_vols', 'dummy_scans'),
             ]),
-            (hmcref_buffer, ds_hmc_boldref_wf, [('boldref', 'inputnode.boldref')]),
             (hmc_boldref_wf, summary, [('outputnode.algo_dummy_scans', 'algo_dummy_scans')]),
             (hmc_boldref_wf, func_fit_reports_wf, [
                 ('outputnode.validation_report', 'inputnode.validation_report'),
@@ -445,6 +446,7 @@ def init_bold_fit_wf(
         )
 
         ds_hmc_wf = init_ds_hmc_wf(
+            source_file=bold_file,
             bids_root=layout.root,
             output_dir=config.execution.fmriprep_dir,
         )
@@ -508,23 +510,32 @@ def init_bold_fit_wf(
             )
 
             itk_mat2txt = pe.Node(ConcatenateXFMs(out_fmt='itk'), name='itk_mat2txt')
+            fmapreg_source_files = pe.Node(
+                niu.Merge(2), name='fmapreg_source_files', run_without_submitting=True
+            )
 
             ds_fmapreg_wf = init_ds_registration_wf(
+                source_file=bold_file,
                 bids_root=layout.root,
                 output_dir=config.execution.fmriprep_dir,
                 source='boldref',
                 dest=re.sub(r'[^a-zA-Z0-9]', '', fieldmap_id),
+                desc='fmap',
                 name='ds_fmapreg_wf',
             )
-            ds_fmapreg_wf.inputs.inputnode.source_files = [bold_file]
 
             workflow.connect([
                 (fmap_select, fmapreg_wf, [
                     ('fmap_ref', 'inputnode.fmap_ref'),
                     ('fmap_mask', 'inputnode.fmap_mask'),
                 ]),
+                (fmapref_buffer, fmapreg_source_files, [('out', 'in1')]),
+                (fmap_select, fmapreg_source_files, [
+                    ('fmap_ref', 'in2'),
+                ]),
                 (fmapreg_wf, itk_mat2txt, [('outputnode.target2fmap_xfm', 'in_xfms')]),
                 (itk_mat2txt, ds_fmapreg_wf, [('out_xfm', 'inputnode.xform')]),
+                (fmapreg_source_files, ds_fmapreg_wf, [('out', 'inputnode.source_files')]),
                 (ds_fmapreg_wf, fmapreg_buffer, [('outputnode.xform', 'boldref2fmap_xfm')]),
             ])  # fmt:skip
         else:
@@ -538,7 +549,7 @@ def init_bold_fit_wf(
     if not coreg_boldref:
         config.loggers.workflow.info('Stage 4: Adding coregistration boldref workflow')
 
-        # Select initial boldref, enhance contrast, and generate mask
+        # 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',
@@ -548,26 +559,30 @@ def init_bold_fit_wf(
             workflow.connect(raw_sbref_wf, 'outputnode.boldref', fmapref_buffer, 'sbref_files')
 
         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
+        )
 
         ds_coreg_boldref_wf = init_ds_boldref_wf(
+            source_file=bold_file,
             bids_root=layout.root,
             output_dir=config.execution.fmriprep_dir,
             desc='coreg',
             name='ds_coreg_boldref_wf',
         )
         ds_boldmask_wf = init_ds_boldmask_wf(
+            source_file=bold_file,
             output_dir=config.execution.fmriprep_dir,
             desc='brain',
             name='ds_boldmask_wf',
         )
-        ds_boldmask_wf.inputs.inputnode.source_files = [bold_file]
 
         workflow.connect([
             (fmapref_buffer, enhance_boldref_wf, [('out', 'inputnode.in_file')]),
-            (hmc_boldref_source_buffer, ds_coreg_boldref_wf, [
-                ('in_file', 'inputnode.source_files'),
-            ]),
+            (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')]),
+            (ds_coreg_boldref_wf, ds_boldmask_wf, [('outputnode.boldref', 'inputnode.source_files')]),
             (ds_boldmask_wf, regref_buffer, [('outputnode.boldmask', 'boldmask')]),
         ])  # fmt:skip
 
@@ -610,6 +625,8 @@ def init_bold_fit_wf(
                 (skullstrip_bold_wf, ds_boldmask_wf, [
                     ('outputnode.mask_file', 'inputnode.boldmask'),
                 ]),
+                (fmapreg_buffer, coreg_ref_source_files, [('boldref2fmap_xfm', 'in2')]),
+                (fmap_select, coreg_ref_source_files, [('fmap_coeff', 'in3')]),
             ])  # fmt:skip
 
             if not boldref2fmap_xform:
@@ -660,10 +677,12 @@ def init_bold_fit_wf(
         )
 
         ds_boldreg_wf = init_ds_registration_wf(
+            source_file=bold_file,
             bids_root=layout.root,
             output_dir=config.execution.fmriprep_dir,
             source='boldref',
             dest='T1w',
+            desc='coreg',
             name='ds_boldreg_wf',
         )
 
diff --git a/fmriprep/workflows/bold/outputs.py b/fmriprep/workflows/bold/outputs.py
index d2785942f..ae4e1db2f 100644
--- a/fmriprep/workflows/bold/outputs.py
+++ b/fmriprep/workflows/bold/outputs.py
@@ -141,6 +141,7 @@ def prepare_timing_parameters(metadata: dict):
 
 def init_func_fit_reports_wf(
     *,
+    source_file: str,
     sdc_correction: bool,
     freesurfer: bool,
     output_dir: str,
@@ -151,6 +152,8 @@ def init_func_fit_reports_wf(
 
     Parameters
     ----------
+    source_file : :class:`str`
+        Input BOLD image, for entity extraction only
     freesurfer : :obj:`bool`
         FreeSurfer was enabled
     output_dir : :obj:`str`
@@ -160,9 +163,6 @@ def init_func_fit_reports_wf(
 
     Inputs
     ------
-    source_file
-        Input BOLD images
-
     std_t1w
         T1w image resampled to standard space
     std_mask
@@ -192,7 +192,6 @@ def init_func_fit_reports_wf(
     workflow = pe.Workflow(name=name)
 
     inputfields = [
-        'source_file',
         'sdc_boldref',
         'coreg_boldref',
         'bold_mask',
@@ -214,6 +213,7 @@ def init_func_fit_reports_wf(
 
     ds_summary = pe.Node(
         DerivativesDataSink(
+            source_file=source_file,
             base_directory=output_dir,
             desc='summary',
             datatype='figures',
@@ -226,6 +226,7 @@ def init_func_fit_reports_wf(
 
     ds_validation = pe.Node(
         DerivativesDataSink(
+            source_file=source_file,
             base_directory=output_dir,
             desc='validation',
             datatype='figures',
@@ -269,11 +270,9 @@ def init_func_fit_reports_wf(
 
     workflow.connect([
         (inputnode, ds_summary, [
-            ('source_file', 'source_file'),
             ('summary_report', 'in_file'),
         ]),
         (inputnode, ds_validation, [
-            ('source_file', 'source_file'),
             ('validation_report', 'in_file'),
         ]),
         (inputnode, t1w_boldref, [
@@ -339,6 +338,7 @@ def init_func_fit_reports_wf(
 
         ds_sdcreg_report = pe.Node(
             DerivativesDataSink(
+                source_file=source_file,
                 base_directory=output_dir,
                 desc='fmapCoreg',
                 suffix='bold',
@@ -361,6 +361,7 @@ def init_func_fit_reports_wf(
 
         ds_sdc_report = pe.Node(
             DerivativesDataSink(
+                source_file=source_file,
                 base_directory=output_dir,
                 desc='sdc',
                 suffix='bold',
@@ -387,14 +388,12 @@ def init_func_fit_reports_wf(
             ]),
             (fmapref_boldref, sdcreg_report, [('output_image', 'moving')]),
             (fmap_boldref, sdcreg_report, [('output_image', 'fieldmap')]),
-            (inputnode, ds_sdcreg_report, [('source_file', 'source_file')]),
             (sdcreg_report, ds_sdcreg_report, [('out_report', 'in_file')]),
             (inputnode, sdc_report, [
                 ('sdc_boldref', 'before'),
                 ('coreg_boldref', 'after'),
             ]),
             (boldref_wm, sdc_report, [('output_image', 'wm_seg')]),
-            (inputnode, ds_sdc_report, [('source_file', 'source_file')]),
             (sdc_report, ds_sdc_report, [('out_report', 'in_file')]),
         ])  # fmt:skip
 
@@ -413,6 +412,7 @@ def init_func_fit_reports_wf(
 
     ds_epi_t1_report = pe.Node(
         DerivativesDataSink(
+            source_file=source_file,
             base_directory=output_dir,
             desc='coreg',
             suffix='bold',
@@ -426,7 +426,6 @@ def init_func_fit_reports_wf(
         (inputnode, epi_t1_report, [('coreg_boldref', 'after')]),
         (t1w_boldref, epi_t1_report, [('output_image', 'before')]),
         (boldref_wm, epi_t1_report, [('output_image', 'wm_seg')]),
-        (inputnode, ds_epi_t1_report, [('source_file', 'source_file')]),
         (epi_t1_report, ds_epi_t1_report, [('out_report', 'in_file')]),
     ])  # fmt:skip
 
@@ -435,6 +434,7 @@ def init_func_fit_reports_wf(
 
 def init_ds_boldref_wf(
     *,
+    source_file: str,
     bids_root,
     output_dir,
     desc: str,
@@ -459,6 +459,7 @@ def init_ds_boldref_wf(
 
     ds_boldref = pe.Node(
         DerivativesDataSink(
+            source_file=source_file,
             base_directory=output_dir,
             desc=desc,
             suffix='boldref',
@@ -471,8 +472,7 @@ def init_ds_boldref_wf(
 
     workflow.connect([
         (inputnode, sources, [('source_files', 'in1')]),
-        (inputnode, ds_boldref, [('boldref', 'in_file'),
-                                 ('source_files', 'source_file')]),
+        (inputnode, ds_boldref, [('boldref', 'in_file')]),
         (sources, ds_boldref, [('out', 'Sources')]),
         (ds_boldref, outputnode, [('out_file', 'boldref')]),
     ])  # fmt:skip
@@ -482,6 +482,7 @@ def init_ds_boldref_wf(
 
 def init_ds_boldmask_wf(
     *,
+    source_file: str,
     output_dir,
     desc: str,
     name='ds_boldmask_wf',
@@ -506,6 +507,7 @@ def init_ds_boldmask_wf(
 
     ds_boldmask = pe.Node(
         DerivativesDataSink(
+            source_file=source_file,
             base_directory=output_dir,
             desc=desc,
             suffix='mask',
@@ -520,7 +522,6 @@ def init_ds_boldmask_wf(
         (inputnode, sources, [('source_files', 'in1')]),
         (inputnode, ds_boldmask, [
             ('boldmask', 'in_file'),
-            ('source_files', 'source_file'),
         ]),
         (sources, ds_boldmask, [('out', 'Sources')]),
         (ds_boldmask, outputnode, [('out_file', 'boldmask')]),
@@ -531,11 +532,13 @@ def init_ds_boldmask_wf(
 
 def init_ds_registration_wf(
     *,
+    source_file: str,
     bids_root: str,
     output_dir: str,
     source: str,
     dest: str,
     name: str,
+    desc: str | None = None,
 ) -> pe.Workflow:
     workflow = pe.Workflow(name=name)
 
@@ -556,8 +559,10 @@ def init_ds_registration_wf(
 
     ds_xform = pe.Node(
         DerivativesDataSink(
+            source_file=source_file,
             base_directory=output_dir,
             mode='image',
+            desc=desc,
             suffix='xfm',
             extension='.txt',
             dismiss_entities=dismiss_echo(['part']),
@@ -572,7 +577,6 @@ def init_ds_registration_wf(
         (inputnode, sources, [('source_files', 'in1')]),
         (inputnode, ds_xform, [
             ('xform', 'in_file'),
-            ('source_files', 'source_file'),
             ('metadata', 'meta_dict'),
         ]),
         (sources, ds_xform, [('out', 'Sources')]),
@@ -584,6 +588,7 @@ def init_ds_registration_wf(
 
 def init_ds_hmc_wf(
     *,
+    source_file: str,
     bids_root,
     output_dir,
     name='ds_hmc_wf',
@@ -607,6 +612,7 @@ def init_ds_hmc_wf(
 
     ds_xforms = pe.Node(
         DerivativesDataSink(
+            source_file=source_file,
             base_directory=output_dir,
             desc='hmc',
             suffix='xfm',
@@ -621,8 +627,7 @@ def init_ds_hmc_wf(
 
     workflow.connect([
         (inputnode, sources, [('source_files', 'in1')]),
-        (inputnode, ds_xforms, [('xforms', 'in_file'),
-                                ('source_files', 'source_file')]),
+        (inputnode, ds_xforms, [('xforms', 'in_file')]),
         (sources, ds_xforms, [('out', 'Sources')]),
         (ds_xforms, outputnode, [('out_file', 'xforms')]),
     ])  # fmt:skip
@@ -632,6 +637,7 @@ def init_ds_hmc_wf(
 
 def init_ds_bold_native_wf(
     *,
+    source_file: str,
     bids_root: str,
     output_dir: str,
     multiecho: bool,
@@ -678,6 +684,7 @@ def init_ds_bold_native_wf(
     if bold_output:
         ds_bold = pe.Node(
             DerivativesDataSink(
+                source_file=source_file,
                 base_directory=output_dir,
                 desc='preproc',
                 compress=True,
@@ -691,7 +698,6 @@ def init_ds_bold_native_wf(
         )
         workflow.connect([
             (inputnode, ds_bold, [
-                ('source_files', 'source_file'),
                 ('bold', 'in_file'),
             ]),
             (sources, ds_bold, [('out', 'Sources')]),
@@ -705,6 +711,7 @@ def init_ds_bold_native_wf(
         }
         ds_t2star = pe.Node(
             DerivativesDataSink(
+                source_file=source_file,
                 base_directory=output_dir,
                 space='boldref',
                 suffix='T2starmap',
@@ -718,7 +725,6 @@ def init_ds_bold_native_wf(
         )
         workflow.connect([
             (inputnode, ds_t2star, [
-                ('source_files', 'source_file'),
                 ('t2star', 'in_file'),
             ]),
             (sources, ds_t2star, [('out', 'Sources')]),
@@ -727,6 +733,7 @@ def init_ds_bold_native_wf(
     if echo_output:
         ds_bold_echos = pe.MapNode(
             DerivativesDataSink(
+                source_file=source_file,
                 base_directory=output_dir,
                 desc='preproc',
                 compress=True,
@@ -742,7 +749,6 @@ def init_ds_bold_native_wf(
         ds_bold_echos.inputs.meta_dict = [{'EchoTime': md['EchoTime']} for md in all_metadata]
         workflow.connect([
             (inputnode, ds_bold_echos, [
-                ('source_files', 'source_file'),
                 ('bold_echos', 'in_file'),
             ]),
         ])  # fmt:skip
@@ -752,6 +758,7 @@ def init_ds_bold_native_wf(
 
 def init_ds_volumes_wf(
     *,
+    source_file: str,
     bids_root: str,
     output_dir: str,
     multiecho: bool,
@@ -800,6 +807,7 @@ def init_ds_volumes_wf(
     # BOLD is pre-resampled
     ds_bold = pe.Node(
         DerivativesDataSink(
+            source_file=source_file,
             base_directory=output_dir,
             desc='preproc',
             compress=True,
@@ -827,7 +835,6 @@ def init_ds_volumes_wf(
             ('boldref2anat_xfm', 'in2'),
         ]),
         (inputnode, ds_bold, [
-            ('source_files', 'source_file'),
             ('bold', 'in_file'),
             ('space', 'space'),
             ('cohort', 'cohort'),
@@ -855,6 +862,7 @@ def init_ds_volumes_wf(
 
     ds_ref = pe.Node(
         DerivativesDataSink(
+            source_file=source_file,
             base_directory=output_dir,
             suffix='boldref',
             compress=True,
@@ -866,6 +874,7 @@ def init_ds_volumes_wf(
     )
     ds_mask = pe.Node(
         DerivativesDataSink(
+            source_file=source_file,
             base_directory=output_dir,
             desc='brain',
             suffix='mask',
@@ -895,6 +904,7 @@ def init_ds_volumes_wf(
         )
         ds_t2star = pe.Node(
             DerivativesDataSink(
+                source_file=source_file,
                 base_directory=output_dir,
                 suffix='T2starmap',
                 compress=True,
@@ -919,7 +929,6 @@ def init_ds_volumes_wf(
             for resampler in resamplers
         ] + [
             (inputnode, datasink, [
-                ('source_files', 'source_file'),
                 ('space', 'space'),
                 ('cohort', 'cohort'),
                 ('resolution', 'resolution'),
@@ -940,6 +949,7 @@ def init_ds_volumes_wf(
 def init_bold_preproc_report_wf(
     mem_gb: float,
     reportlets_dir: str,
+    source_file: str,
     name: str = 'bold_preproc_report_wf',
 ):
     """
@@ -954,10 +964,15 @@ def init_bold_preproc_report_wf(
             :simple_form: yes
 
             from fmriprep.workflows.bold.resampling import init_bold_preproc_report_wf
-            wf = init_bold_preproc_report_wf(mem_gb=1, reportlets_dir='.')
+            wf = init_bold_preproc_report_wf(
+                source_file='sub-01_task-nback_bold.nii.gz',
+                mem_gb=1,
+                reportlets_dir='.')
 
     Parameters
     ----------
+    source_file : :class:`str`
+        Input BOLD image, for entity extraction only
     mem_gb : :obj:`float`
         Size of BOLD file in GB
     reportlets_dir : :obj:`str`
@@ -994,6 +1009,7 @@ def init_bold_preproc_report_wf(
     bold_rpt = pe.Node(SimpleBeforeAfterRPT(), name='bold_rpt', mem_gb=0.1)
     ds_report_bold = pe.Node(
         DerivativesDataSink(
+            source_file=source_file,
             base_directory=reportlets_dir,
             desc='preproc',
             datatype='figures',
diff --git a/pixi.lock b/pixi.lock
index cf4275945..20d82039b 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -298,7 +298,7 @@ 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/8a/a4/c8fbd097440fdb4fb1ef86bbd5789cfc7b2545bf626ac54cbd0e93399e19/nitransforms-25.0.1-py3-none-any.whl
-      - pypi: git+https://github.com/nipreps/niworkflows.git?rev=master#6f223eaa76ec6df17c6725a2b2fd566ad8fe4db7
+      - pypi: git+https://github.com/nipreps/niworkflows.git?rev=master#6586b42542f1c5c16b3999dd6c2d31cafdde6979
       - pypi: https://files.pythonhosted.org/packages/d6/5b/545e9267a1cc080c8a1be2746113a063e34bcdd0f5173fd665a5c13cb234/num2words-0.5.14-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/db/24/552ebea28f0570b9e65e62b50287a273804c9f997cc1c2dcd4e2d64b9e7d/nvidia_ml_py-12.575.51-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/32/ae/ec06af4fe3ee72d16973474f122541746196aaa16cea6f66d18b963c6177/prometheus_client-0.22.1-py3-none-any.whl
@@ -322,7 +322,7 @@ environments:
       - pypi: https://files.pythonhosted.org/packages/1e/db/4254e3eabe8020b458f1a747140d32277ec7a271daf1d235b70dc0b4e6e3/requests-2.32.5-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/e3/30/3c4d035596d3cf444529e0b2953ad0466f6049528a879d27534700580395/rich-14.1.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/87/17/4f0c142525f655729e5710b2763d8306a64b78efaa4488eab5750f45d18d/robustica-0.1.4.tar.gz
-      - pypi: https://files.pythonhosted.org/packages/fb/d5/2a6cdfbcacdda4e48aad8d92da937c6771c99f43ec9b6e10c8906eb86e67/sdcflows-2.13.2-py3-none-any.whl
+      - pypi: git+https://github.com/nipreps/sdcflows.git?rev=main#d95377b9b94df3597c64a919912ae863f639e3c6
       - pypi: https://files.pythonhosted.org/packages/83/11/00d3c3dfc25ad54e731d91449895a79e4bf2384dc3ac01809010ba88f6d5/seaborn-0.13.2-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/e0/f9/0595336914c5619e5f28a1fb793285925a8cd4b432c9da0a987836c7f822/shellingham-1.5.4-py2.py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/e0/bd/400b0bd372a5666addf2540c7358bfc3841b9ce5cdbc5cc4ad2f61627ad8/simplejson-3.20.1-cp312-cp312-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl
@@ -649,7 +649,7 @@ 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/8a/a4/c8fbd097440fdb4fb1ef86bbd5789cfc7b2545bf626ac54cbd0e93399e19/nitransforms-25.0.1-py3-none-any.whl
-      - pypi: git+https://github.com/nipreps/niworkflows.git?rev=master#6f223eaa76ec6df17c6725a2b2fd566ad8fe4db7
+      - pypi: git+https://github.com/nipreps/niworkflows.git?rev=master#6586b42542f1c5c16b3999dd6c2d31cafdde6979
       - pypi: https://files.pythonhosted.org/packages/d2/1d/1b658dbd2b9fa9c4c9f32accbfc0205d532c8c6194dc0f2a4c0428e7128a/nodeenv-1.9.1-py2.py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/d6/5b/545e9267a1cc080c8a1be2746113a063e34bcdd0f5173fd665a5c13cb234/num2words-0.5.14-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/db/24/552ebea28f0570b9e65e62b50287a273804c9f997cc1c2dcd4e2d64b9e7d/nvidia_ml_py-12.575.51-py3-none-any.whl
@@ -677,7 +677,7 @@ environments:
       - pypi: https://files.pythonhosted.org/packages/e3/30/3c4d035596d3cf444529e0b2953ad0466f6049528a879d27534700580395/rich-14.1.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/87/17/4f0c142525f655729e5710b2763d8306a64b78efaa4488eab5750f45d18d/robustica-0.1.4.tar.gz
       - pypi: https://files.pythonhosted.org/packages/47/09/25033198bff89b24d734e6479e39b1968e4c992e82262d61cdccaf11afb9/ruff-0.12.9-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
-      - pypi: https://files.pythonhosted.org/packages/fb/d5/2a6cdfbcacdda4e48aad8d92da937c6771c99f43ec9b6e10c8906eb86e67/sdcflows-2.13.2-py3-none-any.whl
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       - pypi: https://files.pythonhosted.org/packages/83/11/00d3c3dfc25ad54e731d91449895a79e4bf2384dc3ac01809010ba88f6d5/seaborn-0.13.2-py3-none-any.whl
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-  - sdcflows>=2.13.1
+  - sdcflows @ git+https://github.com/nipreps/sdcflows.git@main
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diff --git a/pyproject.toml b/pyproject.toml
index aee0a4da8..b51d934c9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
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