From 7ffffc2fe1204ce34b092c6aa9466dfdf90ea3fa Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Thu, 1 Jun 2023 07:56:12 -0400
Subject: [PATCH 1/2] FIX: Ensure IntendedFor metadata is a subject-relative
 path

---
 sdcflows/utils/wrangler.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/sdcflows/utils/wrangler.py b/sdcflows/utils/wrangler.py
index 2cb9c9414c..ebea2cac3d 100644
--- a/sdcflows/utils/wrangler.py
+++ b/sdcflows/utils/wrangler.py
@@ -459,7 +459,10 @@ def find_estimators(
                 # The new estimator is IntendedFor the individual targets,
                 # even if the EPI file is IntendedFor multiple
                 estimator_md = epi_base_md.copy()
-                estimator_md["IntendedFor"] = intent
+                estimator_md["IntendedFor"] = [
+                    str(Path(pathlike).relative_to(subject_root))
+                    for pathlike in intent
+                ]
                 try:
                     e = fm.FieldmapEstimation(
                         [

From c4ebb64bc38ffdf1adc82602672d0f85330009a6 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Thu, 1 Jun 2023 08:18:18 -0400
Subject: [PATCH 2/2] TEST: Regression test for stringified intents

---
 sdcflows/utils/tests/test_wrangler.py | 54 +++++++++++++++++++++++++++
 1 file changed, 54 insertions(+)

diff --git a/sdcflows/utils/tests/test_wrangler.py b/sdcflows/utils/tests/test_wrangler.py
index 7f79ef4d3c..b162e8c82c 100644
--- a/sdcflows/utils/tests/test_wrangler.py
+++ b/sdcflows/utils/tests/test_wrangler.py
@@ -95,6 +95,43 @@
                     }
                 }
             ]
+        },
+        {
+            "session": "04",
+            "anat": [{"suffix": "T1w", "metadata": {"EchoTime": 1}}],
+            "fmap": [
+                {"suffix": "epi", "dir": "AP", "metadata": {
+                    "EchoTime": 1.2,
+                    "PhaseEncodingDirection": "j-",
+                    "TotalReadoutTime": 0.8,
+                    "IntendedFor": [
+                        "ses-04/func/sub-01_ses-04_task-rest_run-1_bold.nii.gz",
+                        "ses-04/func/sub-01_ses-04_task-rest_run-2_bold.nii.gz",
+                    ],
+                }},
+            ],
+            "func": [
+                {
+                    "task": "rest",
+                    "run": 1,
+                    "suffix": "bold",
+                    "metadata": {
+                        "RepetitionTime": 0.8,
+                        "TotalReadoutTime": 0.5,
+                        "PhaseEncodingDirection": "j"
+                    }
+                },
+                {
+                    "task": "rest",
+                    "run": 2,
+                    "suffix": "bold",
+                    "metadata": {
+                        "RepetitionTime": 0.8,
+                        "TotalReadoutTime": 0.5,
+                        "PhaseEncodingDirection": "j"
+                    }
+                },
+            ]
         }
     ]
 }
@@ -216,3 +253,20 @@ def test_wrangler_filter(tmpdir, name, skeleton, estimations):
     est = find_estimators(layout=layout, subject='01', bids_filters=filters['fmap'])
     assert len(est) == estimations
     clear_registry()
+
+
+def test_single_reverse_pedir(tmp_path):
+    bids_dir = tmp_path / "bids"
+    generate_bids_skeleton(bids_dir, pepolar)
+    layout = gen_layout(bids_dir)
+    est = find_estimators(layout=layout, subject='01', bids_filters={'session': '04'})
+    assert len(est) == 2
+    subject_root = bids_dir / 'sub-01'
+    for estimator in est:
+        assert len(estimator.sources) == 2
+        epi, bold = estimator.sources
+        # Just checking order
+        assert epi.entities['fmap'] == 'epi'
+        # IntendedFor is a list of strings
+        # REGRESSION: The result was a PyBIDS BIDSFile (fmriprep#3020)
+        assert epi.metadata['IntendedFor'] == [str(bold.path.relative_to(subject_root))]