From edd3d8ef45c106f8e4b5ae8d5c7e0375af3b5fbb Mon Sep 17 00:00:00 2001
From: celprov <77437752+celprov@users.noreply.github.com>
Date: Tue, 30 Jan 2024 15:11:12 +0100
Subject: [PATCH] Apply suggestions from code review

Co-authored-by: Oscar Esteban <code@oscaresteban.es>
---
 fmriprep/cli/parser.py              | 3 ++-
 fmriprep/cli/run.py                 | 6 +-----
 fmriprep/data/reports-spec-anat.yml | 4 ++--
 fmriprep/data/reports-spec.yml      | 4 ++--
 4 files changed, 7 insertions(+), 10 deletions(-)

diff --git a/fmriprep/cli/parser.py b/fmriprep/cli/parser.py
index 147e00b22..aa4167e48 100644
--- a/fmriprep/cli/parser.py
+++ b/fmriprep/cli/parser.py
@@ -403,11 +403,12 @@ def _slice_time_ref(value, parser):
     )
     g_outputs.add_argument(
         "--aggregate-session-reports",
+        dest="aggr_ses_reports",
         action="store",
         type=PositiveInt,
         default=4,
         help="Maximum number of sessions aggregated in one subject's visual report. "
-        "If exceeded, visual reports are separated per session.",
+        "If exceeded, visual reports are split by session.",
     )
     g_outputs.add_argument(
         "--medial-surface-nan",
diff --git a/fmriprep/cli/run.py b/fmriprep/cli/run.py
index 206e63db9..cf1f242cf 100644
--- a/fmriprep/cli/run.py
+++ b/fmriprep/cli/run.py
@@ -212,11 +212,7 @@ def main():
         from fmriprep.reports.core import generate_reports
 
         # Generate reports phase
-        session_list = (
-            config.execution.bids_filters["bold"]["session"]
-            if config.execution.bids_filters
-            else None
-        )
+        session_list = config.execution.bids_filters.get("bold", {}).get("session", None)
 
         failed_reports = generate_reports(
             config.execution.participant_label,
diff --git a/fmriprep/data/reports-spec-anat.yml b/fmriprep/data/reports-spec-anat.yml
index 118a06ee1..a65601b34 100644
--- a/fmriprep/data/reports-spec-anat.yml
+++ b/fmriprep/data/reports-spec-anat.yml
@@ -29,7 +29,7 @@ sections:
   reportlets:
   - bids: {datatype: figures, desc: about, suffix: T1w}
   - custom: boilerplate
-    path: '{reportlets_dir}/logs'
+    path: '{output_dir}/logs'
     bibfile: ['fmriprep', 'data/boilerplate.bib']
     caption: |
       <p>We kindly ask to report results preprocessed with this tool using the following boilerplate.</p>
@@ -42,6 +42,6 @@ sections:
       </p>
     title: Methods
   - custom: errors
-    path: '{reportlets_dir}/sub-{subject}/log/{run_uuid}'
+    path: '{output_dir}/sub-{subject}/log/{run_uuid}'
     captions: <em>NiReports</em> may have recorded failure conditions.
     title: Errors
diff --git a/fmriprep/data/reports-spec.yml b/fmriprep/data/reports-spec.yml
index 50062f057..fa5ae17f5 100644
--- a/fmriprep/data/reports-spec.yml
+++ b/fmriprep/data/reports-spec.yml
@@ -180,7 +180,7 @@ sections:
   reportlets:
   - bids: {datatype: figures, desc: about, suffix: T1w}
   - custom: boilerplate
-    path: '{reportlets_dir}/logs'
+    path: '{output_dir}/logs'
     bibfile: ['fmriprep', 'data/boilerplate.bib']
     caption: |
       <p>We kindly ask to report results preprocessed with this tool using the following boilerplate.</p>
@@ -193,6 +193,6 @@ sections:
       </p>
     title: Methods
   - custom: errors
-    path: '{reportlets_dir}/sub-{subject}/log/{run_uuid}'
+    path: '{output_dir}/sub-{subject}/log/{run_uuid}'
     captions: <em>NiReports</em> may have recorded failure conditions.
     title: Errors