FIX: fix petref to report connection and add test

Author: mnoergaard

fmriprep/workflows/pet/confounds.py

@@ -350,18 +350,6 @@ def init_pet_confs_wf(
         mem_gb=DEFAULT_MEMORY_MIN_GB,
     )
 
-    def _last(inlist):
-        return inlist[-1]
-
-    def _select_cols(table):
-        import pandas as pd
-
-        return [
-            col
-            for col in pd.read_table(table, nrows=2).columns
-            if not col.startswith(('a_comp_cor_', 't_comp_cor_', 'std_dvars'))
-        ]
-
     workflow.connect([
         # connect inputnode to each non-anatomical confound node
         (inputnode, dvars, [('pet', 'in_file'),
@@ -619,3 +607,20 @@ def _get_zooms(in_file):
     import nibabel as nb
 
     return tuple(nb.load(in_file).header.get_zooms()[:3])
+
+
+def _last(inlist):
+    """Return the last element of a list."""
+
+    return inlist[-1]
+
+
+def _select_cols(table):
+    """Return confound columns excluding a/tCompCor and std_dvars."""
+    import pandas as pd
+
+    return [
+        col
+        for col in pd.read_table(table, nrows=2).columns
+        if not col.startswith(("a_comp_cor_", "t_comp_cor_", "std_dvars"))
+    ]

fmriprep/workflows/pet/fit.py

@@ -228,6 +228,7 @@ def init_pet_fit_wf(
             ('subjects_dir', 'inputnode.subjects_dir'),
             ('subject_id', 'inputnode.subject_id'),
         ]),
+        (petref_buffer, func_fit_reports_wf, [('petref', 'inputnode.petref')]),
         (outputnode, func_fit_reports_wf, [
             ('pet_mask', 'inputnode.pet_mask'),
             ('petref2anat_xfm', 'inputnode.petref2anat_xfm'),

fmriprep/workflows/pet/tests/test_fit.py

@@ -154,3 +154,17 @@ def test_pet_fit_mask_connections(bids_root: Path, tmp_path: Path):
 
     ds_edge = wf._graph.get_edge_data(merge_mask, wf.get_node('ds_petmask_wf'))
     assert ('out', 'inputnode.petmask') in ds_edge['connect']
+
+
+def test_petref_report_connections(bids_root: Path, tmp_path: Path):
+    """Ensure the PET reference is passed to the reports workflow."""
+    pet_file = str(bids_root / 'sub-01' / 'pet' / 'sub-01_task-rest_run-1_pet.nii.gz')
+    img = nb.Nifti1Image(np.zeros((2, 2, 2, 1)), np.eye(4))
+    img.to_filename(pet_file)
+
+    with mock_config(bids_dir=bids_root):
+        wf = init_pet_fit_wf(pet_file=pet_file, precomputed={}, omp_nthreads=1)
+
+    petref_buffer = wf.get_node('petref_buffer')
+    edge = wf._graph.get_edge_data(petref_buffer, wf.get_node('func_fit_reports_wf'))
+    assert ('petref', 'inputnode.petref') in edge['connect']