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Merge tag '2.13.2'
2.13.2 (July 28, 2025) Patch release in the 2.13.x series. This includes a fix for cases where a scan contributes to multiple `B0FieldIdentifier`s. * [FIX] Fixes conditions of overlapping B0FieldIdentifier, resulting in no estimators (#497)
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‎CHANGES.rst‎

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Original file line numberDiff line numberDiff line change
@@ -1,11 +1,21 @@
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2.13.1 (Jane 12, 2025)
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2.13.2 (July 28, 2025)
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======================
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Patch release in the 2.13.x series.
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This includes a fix for cases where a scan contributes to multiple ``B0FieldIdentifier``\s.
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* [FIX] Fixes conditions of overlapping B0FieldIdentifier, resulting in no estimators (#497)
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2.13.1 (June 12, 2025)
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======================
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Patch release in the 2.13.x series.
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This includes a fix to ``init_fmap_preproc_wf`` node naming.
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* FIX: Use the sanitized id when naming through nipype (#495)
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2.13.0 (May 15, 2025)
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=====================
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Feature release in the 2.13.x series.

‎sdcflows/utils/tests/test_wrangler.py‎

Lines changed: 152 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -202,6 +202,146 @@ def gen_layout(bids_dir, database_dir=None):
202202
}
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205+
pepolar_b0ids = {
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'01': [
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{
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'session': '01',
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'anat': [{'suffix': 'T1w', 'metadata': {'EchoTime': 1}}],
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'func': [
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{
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'task': 'rest',
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'run': 1,
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'suffix': 'bold',
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'metadata': {
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'RepetitionTime': 0.8,
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'TotalReadoutTime': 0.5,
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'PhaseEncodingDirection': 'j',
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'B0FieldIdentifier': 'b0_pepolar',
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'B0FieldSource': 'b0_pepolar',
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},
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},
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{
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'task': 'rest',
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'run': 2,
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'suffix': 'bold',
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'metadata': {
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'RepetitionTime': 0.8,
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'TotalReadoutTime': 0.5,
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'PhaseEncodingDirection': 'j-',
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'B0FieldIdentifier': 'b0_pepolar',
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'B0FieldSource': 'b0_pepolar',
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},
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},
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],
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},
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{
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'session': '02',
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'anat': [{'suffix': 'T1w', 'metadata': {'EchoTime': 1}}],
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'func': [
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{
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'task': 'rest',
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'run': 1,
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'suffix': 'bold',
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'metadata': {
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'RepetitionTime': 0.8,
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'TotalReadoutTime': 0.5,
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'PhaseEncodingDirection': 'j',
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'B0FieldSource': 'b0_pepolar',
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},
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},
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{
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'task': 'rest',
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'run': 2,
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'suffix': 'bold',
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'metadata': {
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'RepetitionTime': 0.8,
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'TotalReadoutTime': 0.5,
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'PhaseEncodingDirection': 'j-',
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'B0FieldSource': 'b0_pepolar',
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},
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},
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{
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'task': 'rest',
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'run': 1,
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'suffix': 'sbref',
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'metadata': {
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'RepetitionTime': 0.8,
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'TotalReadoutTime': 0.5,
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'PhaseEncodingDirection': 'j',
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'B0FieldIdentifier': 'b0_pepolar',
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'B0FieldSource': 'b0_pepolar',
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},
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},
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{
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'task': 'rest',
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'run': 2,
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'suffix': 'sbref',
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'metadata': {
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'RepetitionTime': 0.8,
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'TotalReadoutTime': 0.5,
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'PhaseEncodingDirection': 'j-',
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'B0FieldIdentifier': 'b0_pepolar',
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'B0FieldSource': 'b0_pepolar',
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},
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},
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],
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},
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{
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'session': '03',
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'anat': [{'suffix': 'T1w', 'metadata': {'EchoTime': 1}}],
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'func': [
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{
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'task': 'rest',
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'run': 1,
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'suffix': 'bold',
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'metadata': {
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'RepetitionTime': 0.8,
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'TotalReadoutTime': 0.5,
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'PhaseEncodingDirection': 'j',
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'B0FieldSource': 'b0_pepolar',
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},
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},
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{
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'task': 'rest',
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'run': 2,
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'suffix': 'bold',
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'metadata': {
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'RepetitionTime': 0.8,
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'TotalReadoutTime': 0.5,
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'PhaseEncodingDirection': 'j-',
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'B0FieldSource': 'b0_pepolar',
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},
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},
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{
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'task': 'rest',
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'run': 1,
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'suffix': 'sbref',
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'metadata': {
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'RepetitionTime': 0.8,
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'TotalReadoutTime': 0.5,
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'PhaseEncodingDirection': 'j',
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'B0FieldIdentifier': ['b0_pepolar', 'b0_pepolar_dup'],
324+
'B0FieldSource': 'b0_pepolar',
325+
},
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},
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{
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'task': 'rest',
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'run': 2,
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'suffix': 'sbref',
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'metadata': {
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'RepetitionTime': 0.8,
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'TotalReadoutTime': 0.5,
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'PhaseEncodingDirection': 'j-',
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'B0FieldIdentifier': ['b0_pepolar', 'b0_pepolar_dup'],
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'B0FieldSource': 'b0_pepolar',
337+
},
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},
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],
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},
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]
342+
}
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205345
phasediff = {
206346
'01': [
207347
{
@@ -304,26 +444,28 @@ def gen_layout(bids_dir, database_dir=None):
304444

305445

306446
@pytest.mark.parametrize(
307-
'name,skeleton,estimations',
447+
'name,skeleton,estimations,bids_filters',
308448
[
309-
('pepolar', pepolar, 1),
310-
('phasediff', phasediff, 1),
449+
('pepolar', pepolar, 1, 'fmap'),
450+
('pepolar_b0ids', pepolar_b0ids, 1, 'bold'),
451+
('phasediff', phasediff, 1, 'fmap'),
311452
],
312453
)
313-
def test_wrangler_filter(tmpdir, name, skeleton, estimations):
454+
def test_wrangler_filter(tmpdir, name, skeleton, estimations, bids_filters):
314455
bids_dir = str(tmpdir / name)
315456
generate_bids_skeleton(bids_dir, skeleton)
316457
layout = gen_layout(bids_dir)
317-
est = find_estimators(layout=layout, subject='01', bids_filters=filters['fmap'])
458+
est = find_estimators(layout=layout, subject='01', bids_filters=filters[bids_filters])
318459
assert len(est) == estimations
319460
clear_registry()
320461

321462

322463
@pytest.mark.parametrize(
323-
'name,skeleton,total_estimations',
464+
'name,skeleton,total_estimations,test_auto',
324465
[
325-
('pepolar', pepolar, 5),
326-
('phasediff', phasediff, 3),
466+
('pepolar', pepolar, 5, True),
467+
('pepolar_b0ids', pepolar_b0ids, 2, False),
468+
('phasediff', phasediff, 3, True),
327469
],
328470
)
329471
@pytest.mark.parametrize(
@@ -335,7 +477,7 @@ def test_wrangler_filter(tmpdir, name, skeleton, estimations):
335477
(None, None),
336478
],
337479
)
338-
def test_wrangler_URIs(tmpdir, name, skeleton, session, estimations, total_estimations):
480+
def test_wrangler_URIs(tmpdir, name, skeleton, session, estimations, total_estimations, test_auto):
339481
bids_dir = str(tmpdir / name)
340482
generate_bids_skeleton(bids_dir, skeleton)
341483
layout = gen_layout(bids_dir)
@@ -345,7 +487,7 @@ def test_wrangler_URIs(tmpdir, name, skeleton, session, estimations, total_estim
345487
sessions=[session] if session else None,
346488
)
347489
assert len(est) == estimations or total_estimations
348-
if session:
490+
if session and test_auto:
349491
bold = layout.get(session=session, suffix='bold', extension='.nii.gz')[0]
350492
intended_rel = re.sub(r'^sub-[a-zA-Z0-9]*/', '', str(Path(bold).relative_to(layout.root)))
351493
b0_id = get_identifier(intended_rel)

‎sdcflows/utils/wrangler.py‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -377,7 +377,8 @@ def find_estimators(
377377
[
378378
fm.FieldmapFile(fmap.path, metadata=fmap.get_metadata())
379379
for fmap in bare_ids + listed_ids
380-
]
380+
],
381+
bids_id=b0_id,
381382
)
382383
except (ValueError, TypeError) as err:
383384
_log_debug_estimator_fail(

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