Actually pass argument...

Author: effigies

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_file,
             bids_root=str(config.execution.bids_dir),
             output_dir=fmriprep_dir,
             bold_output=boldref_out,
@@ -372,7 +373,6 @@ 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
@@ -416,6 +416,7 @@ def init_bold_wf(
     # 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,
@@ -453,6 +454,7 @@ 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,

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',
@@ -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,
         )
@@ -513,6 +515,7 @@ def init_bold_fit_wf(
             )
 
             ds_fmapreg_wf = init_ds_registration_wf(
+                source_file=bold_file,
                 bids_root=layout.root,
                 output_dir=config.execution.fmriprep_dir,
                 source='boldref',
@@ -561,12 +564,14 @@ def init_bold_fit_wf(
         )
 
         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',
@@ -672,6 +677,7 @@ 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',

fmriprep/workflows/bold/outputs.py

@@ -270,11 +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, [
@@ -390,14 +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
 
@@ -430,7 +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