FIX: Use sanitized fieldmap naming (#3471)

Addresses #3468

Changes were made in sdcflows, but forgotten here...

Replaces #3470

Author: mgxd

fmriprep/workflows/base.py

@@ -692,7 +692,7 @@ def init_single_subject_wf(subject_id: str):
                 if len(set(suffices)) == 1 or (
                     len(suffices) == 2 and all(suf in ('epi', 'bold', 'sbref') for suf in suffices)
                 ):
-                    wf_inputs = getattr(fmap_wf.inputs, f'in_{estimator.bids_id}')
+                    wf_inputs = getattr(fmap_wf.inputs, f'in_{estimator.sanitized_id}')
                     wf_inputs.in_data = [str(s.path) for s in estimator.sources]
                     wf_inputs.metadata = [s.metadata for s in estimator.sources]
                 else:
@@ -710,7 +710,7 @@ def init_single_subject_wf(subject_id: str):
                     debug=config.execution.sloppy,
                     auto_bold_nss=True,
                     t1w_inversion=False,
-                    name=f'syn_preprocessing_{estimator.bids_id}',
+                    name=f'syn_preprocessing_{estimator.sanitized_id}',
                 )
                 syn_preprocessing_wf.inputs.inputnode.in_epis = sources
                 syn_preprocessing_wf.inputs.inputnode.in_meta = source_meta
@@ -724,11 +724,11 @@ def init_single_subject_wf(subject_id: str):
                         ('std2anat_xfm', 'inputnode.std2anat_xfm'),
                     ]),
                     (syn_preprocessing_wf, fmap_wf, [
-                        ('outputnode.epi_ref', f'in_{estimator.bids_id}.epi_ref'),
-                        ('outputnode.epi_mask', f'in_{estimator.bids_id}.epi_mask'),
-                        ('outputnode.anat_ref', f'in_{estimator.bids_id}.anat_ref'),
-                        ('outputnode.anat_mask', f'in_{estimator.bids_id}.anat_mask'),
-                        ('outputnode.sd_prior', f'in_{estimator.bids_id}.sd_prior'),
+                        ('outputnode.epi_ref', f'in_{estimator.sanitized_id}.epi_ref'),
+                        ('outputnode.epi_mask', f'in_{estimator.sanitized_id}.epi_mask'),
+                        ('outputnode.anat_ref', f'in_{estimator.sanitized_id}.anat_ref'),
+                        ('outputnode.anat_mask', f'in_{estimator.sanitized_id}.anat_mask'),
+                        ('outputnode.sd_prior', f'in_{estimator.sanitized_id}.sd_prior'),
                     ]),
                 ])  # fmt:skip
 

fmriprep/workflows/tests/test_base.py

@@ -60,12 +60,12 @@
             {'suffix': 'magnitude1', 'metadata': {'EchoTime': 0.005}},
             {
                 'suffix': 'epi',
-                'direction': 'PA',
+                'dir': 'PA',
                 'metadata': {'PhaseEncodingDirection': 'j', 'TotalReadoutTime': 0.6},
             },
             {
                 'suffix': 'epi',
-                'direction': 'AP',
+                'dir': 'AP',
                 'metadata': {'PhaseEncodingDirection': 'j-', 'TotalReadoutTime': 0.6},
             },
         ],
@@ -230,6 +230,25 @@ def test_init_fmriprep_wf(
     generate_expanded_graph(wf._create_flat_graph())
 
 
+def test_init_fmriprep_wf_sanitize_fmaps(tmp_path):
+    bids_dir = tmp_path / 'bids'
+
+    spec = deepcopy(BASE_LAYOUT)
+    spec['01']['func'][0]['metadata']['B0FieldSource'] = 'epi<<run1>>'
+    spec['01']['fmap'][2]['metadata']['B0FieldIdentifier'] = 'epi<<run1>>'
+    spec['01']['fmap'][3]['metadata']['B0FieldIdentifier'] = 'epi<<run1>>'
+    del spec['01']['func'][4:]
+
+    generate_bids_skeleton(bids_dir, spec)
+    img = nb.Nifti1Image(np.zeros((10, 10, 10, 10)), np.eye(4))
+    for img_path in bids_dir.glob('sub-01/*/*.nii.gz'):
+        img.to_filename(img_path)
+
+    with mock_config(bids_dir=bids_dir):
+        wf = init_fmriprep_wf()
+    generate_expanded_graph(wf._create_flat_graph())
+
+
 def test_get_estimator_none(tmp_path):
     bids_dir = tmp_path / 'bids'
 
@@ -265,6 +284,25 @@ def test_get_estimator_b0field_and_intendedfor(tmp_path):
     )
 
     assert get_estimator(layout, bold_files[0]) == ('epi',)
+    # if B0FieldIdentifiers are found, IntendedFor will not be used
+    assert get_estimator(layout, bold_files[1]) == ()
+
+
+def test_get_estimator_intendedfor(tmp_path):
+    bids_dir = tmp_path / 'bids'
+
+    # Set B0FieldSource for run 1
+    spec = deepcopy(BASE_LAYOUT)
+    spec['01']['fmap'][0]['metadata']['IntendedFor'] = 'func/sub-01_task-rest_run-2_bold.nii.gz'
+
+    generate_bids_skeleton(bids_dir, spec)
+    layout = bids.BIDSLayout(bids_dir)
+    _ = find_estimators(layout=layout, subject='01')
+
+    bold_files = sorted(
+        layout.get(suffix='bold', task='rest', extension='.nii.gz', return_type='file')
+    )
+
     assert get_estimator(layout, bold_files[1]) == ('auto_00000',)
 
 

pyproject.toml

@@ -34,7 +34,7 @@ dependencies = [
     "psutil >= 5.4",
     "pybids >= 0.16",
     "requests >= 2.27",
-    "sdcflows >= 2.13.0",
+    "sdcflows >= 2.13.1",
     "smriprep >= 0.18.0",
     "tedana >= 25.0.0",
     "templateflow >= 24.2.2",