From 64269beeec9a92c335c38d54c6e74960cfb09dd5 Mon Sep 17 00:00:00 2001
From: Patrick Sadil <psadil@gmail.com>
Date: Wed, 2 Oct 2024 10:59:07 -0400
Subject: [PATCH 1/3] let fieldmap_id be optional

---
 fmriprep/utils/bids.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/fmriprep/utils/bids.py b/fmriprep/utils/bids.py
index b2927547..3c12ff5d 100644
--- a/fmriprep/utils/bids.py
+++ b/fmriprep/utils/bids.py
@@ -41,7 +41,7 @@
 def collect_derivatives(
     derivatives_dir: Path,
     entities: dict,
-    fieldmap_id: str | None,
+    fieldmap_id: str | None = None,
     spec: dict | None = None,
     patterns: list[str] | None = None,
 ):

From 0c2e1b58f9034fd33b01f632d4272d52401e5878 Mon Sep 17 00:00:00 2001
From: Patrick Sadil <psadil@gmail.com>
Date: Wed, 2 Oct 2024 11:00:23 -0400
Subject: [PATCH 2/3] override matched provided entities with baseline spec
 query

---
 fmriprep/utils/bids.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/fmriprep/utils/bids.py b/fmriprep/utils/bids.py
index 3c12ff5d..5ca78d91 100644
--- a/fmriprep/utils/bids.py
+++ b/fmriprep/utils/bids.py
@@ -62,7 +62,7 @@ def collect_derivatives(
 
     # search for both boldrefs
     for k, q in spec['baseline'].items():
-        query = {**q, **entities}
+        query = {**entities, **q}
         item = layout.get(return_type='filename', **query)
         if not item:
             continue

From c568a7beb682dddb8e93a31ea1c9f9a73d72e20f Mon Sep 17 00:00:00 2001
From: Patrick Sadil <psadil@gmail.com>
Date: Wed, 2 Oct 2024 11:27:51 -0400
Subject: [PATCH 3/3] handle merge conflicts

---
 fmriprep/utils/tests/test_derivative_cache.py | 22 +++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/fmriprep/utils/tests/test_derivative_cache.py b/fmriprep/utils/tests/test_derivative_cache.py
index 1a2c59ac..87382f73 100644
--- a/fmriprep/utils/tests/test_derivative_cache.py
+++ b/fmriprep/utils/tests/test_derivative_cache.py
@@ -5,6 +5,28 @@
 from fmriprep.utils import bids
 
 
+@pytest.mark.parametrize('desc', ['hmc', 'coreg'])
+def test_baseline_found_as_str(tmp_path: Path, desc: str):
+    subject = '0'
+    task = 'rest'
+
+    to_find = tmp_path.joinpath(
+        f'sub-{subject}', 'func', f'sub-{subject}_task-{task}_desc-{desc}_boldref.nii.gz'
+    )
+    to_find.parent.mkdir(parents=True)
+    to_find.touch()
+
+    entities = {
+        'subject': subject,
+        'task': task,
+        'suffix': 'bold',
+        'extension': '.nii.gz',
+    }
+
+    derivs = bids.collect_derivatives(derivatives_dir=tmp_path, entities=entities)
+    assert dict(derivs) == {f'{desc}_boldref': str(to_find), 'transforms': {}}
+
+
 @pytest.mark.parametrize('xfm', ['boldref2fmap', 'boldref2anat', 'hmc'])
 def test_transforms_found_as_str(tmp_path: Path, xfm: str):
     subject = '0'