rf: Use merge buffers to collect source files

Author: effigies

fmriprep/workflows/bold/fit.py

@@ -316,19 +316,6 @@ def init_bold_fit_wf(
         config.loggers.workflow.debug(f'Reusing coregistration reference: {coreg_boldref}')
     fmapref_buffer.inputs.sbref_files = sbref_files
 
-    # If sbref files are available, add them to the list of sources
-    boldref_source_files = [bold_file]
-    if sbref_files:
-        boldref_source_files.append(sbref_files[0])
-
-        if 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')
-
     summary = pe.Node(
         FunctionalSummary(
             distortion_correction='None',  # Can override with connection
@@ -521,23 +508,31 @@ 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(
                 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 = boldref_source_files
 
             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:
@@ -551,7 +546,19 @@ 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_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(
             bids_root=layout.root,
@@ -564,14 +571,13 @@ def init_bold_fit_wf(
             desc='brain',
             name='ds_boldmask_wf',
         )
-        ds_boldmask_wf.inputs.inputnode.source_files = boldref_source_files
 
         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
 
@@ -614,6 +620,8 @@ 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:
@@ -668,6 +676,7 @@ def init_bold_fit_wf(
             output_dir=config.execution.fmriprep_dir,
             source='boldref',
             dest='T1w',
+            desc='coreg',
             name='ds_boldreg_wf',
         )
 

fmriprep/workflows/bold/outputs.py

@@ -536,6 +536,7 @@ def init_ds_registration_wf(
     source: str,
     dest: str,
     name: str,
+    desc: str | None = None,
 ) -> pe.Workflow:
     workflow = pe.Workflow(name=name)
 
@@ -558,6 +559,7 @@ def init_ds_registration_wf(
         DerivativesDataSink(
             base_directory=output_dir,
             mode='image',
+            desc=desc,
             suffix='xfm',
             extension='.txt',
             dismiss_entities=dismiss_echo(['part']),