fix: Retrieve fieldmaps and HMC boldref from output directory

Author: effigies

fmriprep/workflows/base.py

@@ -726,11 +726,20 @@ def init_single_subject_wf(
             if node.split('.')[-1].startswith('ds_'):
                 fmap_wf.get_node(node).interface.out_path_base = ''
 
+        # Retrieve fieldmap files from the derivatives directory
+        # TODO: SDCFlows should route these files through the outputnode
+        output_map = {
+            'fmap': 'fmap_derivatives_wf.ds_fieldmap.out_file',
+            'fmap_ref': 'fmap_derivatives_wf.ds_reference.out_file',
+            'fmap_coeff': 'fmap_derivatives_wf.ds_coeff.out_file',
+        }
+
         workflow.connect([
             (fmap_wf, fmap_buffers[field], [
                 # We get "sdc_method" as "method" from estimator workflows
                 # All else stays the same, and no other sdc_ prefixes are used
-                (f'outputnode.{field.removeprefix("sdc_")}', 'in2'),
+                (output_map[field.removeprefix('sdc_')], 'in2')
+                # (f'outputnode.{field.removeprefix("sdc_")}', 'in2'),
             ])
             for field in fmap_buffers
         ])  # fmt:skip

fmriprep/workflows/bold/fit.py

@@ -408,12 +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'),