rf: Populate buffers with precomputed derivatives early

Author: effigies

fmriprep/workflows/bold/fit.py

@@ -304,6 +304,13 @@ def init_bold_fit_wf(
         niu.IdentityInterface(fields=['boldref', 'boldmask']), name='regref_buffer'
     )
 
+    # Set default buffer values; can be overridden by workflows
+    hmcref_buffer.inputs.boldref = precomputed.get('hmc_boldref')
+    fmapref_buffer.inputs.sbref_files = sbref_files
+    hmc_buffer.inputs.hmc_xforms = hmc_xforms
+    fmapreg_buffer.inputs.boldref2fmap_xfm = boldref2fmap_xform
+    regref_buffer.inputs.boldref = precomputed.get('coreg_boldref')
+
     summary = pe.Node(
         FunctionalSummary(
             distortion_correction='None',  # Can override with connection
@@ -342,7 +349,6 @@ def init_bold_fit_wf(
         output_dir=config.execution.fmriprep_dir,
     )
 
-    # fmt:off
     workflow.connect([
         (hmcref_buffer, outputnode, [
             ('boldref', 'hmc_boldref'),
@@ -371,8 +377,7 @@ def init_bold_fit_wf(
             ('boldref2anat_xfm', 'inputnode.boldref2anat_xfm'),
         ]),
         (summary, func_fit_reports_wf, [('out_report', 'inputnode.summary_report')]),
-    ])
-    # fmt:on
+    ])  # fmt:skip
 
     # Stage 1: Generate motion correction boldref
     hmc_boldref_source_buffer = pe.Node(
@@ -413,7 +418,6 @@ def init_bold_fit_wf(
         ])  # fmt:skip
     else:
         config.loggers.workflow.info('Found HMC boldref - skipping Stage 1')
-        hmcref_buffer.inputs.boldref = precomputed['hmc_boldref']
 
         validation_and_dummies_wf = init_validation_and_dummies_wf(bold_file=bold_file)
 
@@ -451,15 +455,13 @@ def init_bold_fit_wf(
         ])  # fmt:skip
     else:
         config.loggers.workflow.info('Found motion correction transforms - skipping Stage 2')
-        hmc_buffer.inputs.hmc_xforms = hmc_xforms
 
     # Stage 3: Create coregistration reference
     # Fieldmap correction only happens during fit if this stage is needed
     if not have_coregref:
         config.loggers.workflow.info('Stage 3: Adding coregistration boldref workflow')
 
         # Select initial boldref, enhance contrast, and generate mask
-        fmapref_buffer.inputs.sbref_files = sbref_files
         if sbref_files and nb.load(sbref_files[0]).ndim > 3:
             raw_sbref_wf = init_raw_boldref_wf(
                 name='raw_sbref_wf',
@@ -523,7 +525,6 @@ def init_bold_fit_wf(
                 )
                 ds_fmapreg_wf.inputs.inputnode.source_files = [bold_file]
 
-                # fmt:off
                 workflow.connect([
                     (enhance_boldref_wf, fmapreg_wf, [
                         ('outputnode.bias_corrected_file', 'inputnode.target_ref'),
@@ -536,10 +537,7 @@ def init_bold_fit_wf(
                     (fmapreg_wf, itk_mat2txt, [('outputnode.target2fmap_xfm', 'in_xfms')]),
                     (itk_mat2txt, ds_fmapreg_wf, [('out_xfm', 'inputnode.xform')]),
                     (ds_fmapreg_wf, fmapreg_buffer, [('outputnode.xform', 'boldref2fmap_xfm')]),
-                ])
-                # fmt:on
-            else:
-                fmapreg_buffer.inputs.boldref2fmap_xfm = boldref2fmap_xform
+                ])  # fmt:skip
 
             unwarp_wf = init_unwarp_wf(
                 free_mem=config.environment.free_mem,
@@ -598,7 +596,6 @@ def init_bold_fit_wf(
             ])  # fmt:skip
     else:
         config.loggers.workflow.info('Found coregistration reference - skipping Stage 3')
-        regref_buffer.inputs.boldref = precomputed['coreg_boldref']
 
         # TODO: Allow precomputed bold masks to be passed
         # Also needs consideration for how it interacts above