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: |

We kindly ask to report results preprocessed with this tool using the following boilerplate.

@@ -42,6 +42,6 @@ sections:

title: Methods - custom: errors - path: '{reportlets_dir}/sub-{subject}/log/{run_uuid}' + path: '{output_dir}/sub-{subject}/log/{run_uuid}' captions: NiReports 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: |

We kindly ask to report results preprocessed with this tool using the following boilerplate.

@@ -193,6 +193,6 @@ sections:

title: Methods - custom: errors - path: '{reportlets_dir}/sub-{subject}/log/{run_uuid}' + path: '{output_dir}/sub-{subject}/log/{run_uuid}' captions: NiReports may have recorded failure conditions. title: Errors