From a5c96a3d9459fae7427648cfc0bbc982b27f4fa5 Mon Sep 17 00:00:00 2001
From: mnoergaard <martin.noergaard@nru.dk>
Date: Mon, 24 Nov 2025 13:39:43 +0100
Subject: [PATCH 1/2] ENH: Fix subject ID conflicts in visualizations

---
 petprep/reports/core.py               | 17 ++++++++++++++++-
 petprep/reports/tests/test_reports.py | 27 +++++++++++++++++++++++++++
 2 files changed, 43 insertions(+), 1 deletion(-)

diff --git a/petprep/reports/core.py b/petprep/reports/core.py
index a4b83f8c..0199ed01 100644
--- a/petprep/reports/core.py
+++ b/petprep/reports/core.py
@@ -82,6 +82,21 @@ def generate_reports(
     errors = []
     for subject_label in subject_list:
         subject_label = subject_label.removeprefix('sub-')
+
+        subject_reportlets_dir = reportlets_dir
+        if reportlets_dir is not None:
+            subject_reportlets_dir = next(
+                (
+                    candidate
+                    for candidate in (
+                        reportlets_dir / 'petprep' / f'sub-{subject_label}',
+                        reportlets_dir / f'sub-{subject_label}',
+                        reportlets_dir,
+                    )
+                    if candidate.exists()
+                ),
+                reportlets_dir,
+            )
         # The number of sessions is intentionally not based on session_list but
         # on the total number of sessions, because I want the final derivatives
         # folder to be the same whether sessions were run one at a time or all-together.
@@ -106,7 +121,7 @@ def generate_reports(
             run_uuid,
             bootstrap_file=bootstrap_file,
             out_filename=html_report,
-            reportlets_dir=reportlets_dir,
+            reportlets_dir=subject_reportlets_dir,
             errorname=f'report-{run_uuid}-{subject_label}.err',
             subject=subject_label,
         )
diff --git a/petprep/reports/tests/test_reports.py b/petprep/reports/tests/test_reports.py
index 75c122fd..e8152392 100644
--- a/petprep/reports/tests/test_reports.py
+++ b/petprep/reports/tests/test_reports.py
@@ -5,6 +5,7 @@
 from bids.layout import BIDSLayout
 
 from petprep.reports.core import generate_reports
+import petprep.reports.core as core
 
 from ... import config, data
 
@@ -146,3 +147,29 @@ def test_pet_report(tmp_path, monkeypatch):
     assert html_file.is_file()
     html_content = html_file.read_text()
     assert '<div id="PET"' in html_content
+
+
+def test_reportlets_dir_scoped_to_subject(tmp_path, monkeypatch):
+    work_dir = tmp_path / 'work'
+    target = work_dir / 'reportlets' / 'petprep' / 'sub-02'
+    target.mkdir(parents=True)
+    (work_dir / 'reportlets' / 'petprep' / 'sub-002').mkdir(parents=True)
+
+    recorded_reportlets = []
+
+    def _record_reportlets_dir(*args, reportlets_dir=None, **kwargs):
+        recorded_reportlets.append(reportlets_dir)
+        return None
+
+    monkeypatch.setattr(core, 'run_reports', _record_reportlets_dir)
+    monkeypatch.setattr(config.execution, 'aggr_ses_reports', 4)
+
+    class _Layout:
+        def get_sessions(self, subject=None):
+            return []
+
+    monkeypatch.setattr(config.execution, 'layout', _Layout())
+
+    generate_reports(['02'], tmp_path, 'fake', work_dir=work_dir)
+
+    assert recorded_reportlets == [target]

From 64797593cfbab018d8866287d7840cae99da9ed9 Mon Sep 17 00:00:00 2001
From: mnoergaard <martin.noergaard@nru.dk>
Date: Mon, 24 Nov 2025 13:41:56 +0100
Subject: [PATCH 2/2] FIX: style

---
 petprep/reports/tests/test_reports.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/petprep/reports/tests/test_reports.py b/petprep/reports/tests/test_reports.py
index e8152392..b7457ff4 100644
--- a/petprep/reports/tests/test_reports.py
+++ b/petprep/reports/tests/test_reports.py
@@ -4,8 +4,8 @@
 import pytest
 from bids.layout import BIDSLayout
 
-from petprep.reports.core import generate_reports
 import petprep.reports.core as core
+from petprep.reports.core import generate_reports
 
 from ... import config, data