ENH: Add PET report support in fmriprep

Author: mnoergaard

fmriprep/cli/workflow.py

@@ -86,7 +86,7 @@ def build_workflow(config_file, retval):
     if config.execution.reports_only:
         build_log.log(25, 'Running --reports-only on participants %s', ', '.join(subject_list))
         session_list = (
-            config.execution.bids_filters.get('bold', {}).get('session')
+            config.execution.bids_filters.get('pet', config.execution.bids_filters.get('bold', {})).get('session')
             if config.execution.bids_filters
             else None
         )

fmriprep/data/reports-spec-pet.yml

@@ -0,0 +1,14 @@
+package: fmriprep
+title: PET report for participant '{subject}', session '{session}' - fMRIPrep
+sections:
+- name: PET
+  ordering: session
+  reportlets:
+  - bids: {datatype: figures, desc: summary, suffix: pet}
+  - bids: {datatype: figures, desc: validation, suffix: pet}
+  - bids: {datatype: figures, desc: carpetplot, suffix: pet}
+  - bids: {datatype: figures, desc: confoundcorr, suffix: pet}
+  - bids: {datatype: figures, suffix: pet}
+- name: About
+  reportlets:
+  - bids: {datatype: figures, desc: about, suffix: T1w}

fmriprep/data/reports-spec.yml

@@ -106,6 +106,14 @@ sections:
       effects and can inform decisions about feature orthogonalization prior to
       confound regression.
     subtitle: Correlations among nuisance regressors
+- name: PET
+  ordering: session
+  reportlets:
+  - bids: {datatype: figures, desc: summary, suffix: pet}
+  - bids: {datatype: figures, desc: validation, suffix: pet}
+  - bids: {datatype: figures, desc: carpetplot, suffix: pet}
+  - bids: {datatype: figures, desc: confoundcorr, suffix: pet}
+  - bids: {datatype: figures, suffix: pet}
 - name: About
   nested: true
   reportlets:

fmriprep/reports/core.py

@@ -119,7 +119,7 @@ def generate_reports(
             # we separate the functional reports per session
             if session_list is None:
                 all_filters = config.execution.bids_filters or {}
-                filters = all_filters.get('bold', {})
+                filters = all_filters.get("pet", all_filters.get("bold", {}))
                 session_list = config.execution.layout.get_sessions(
                     subject=subject_label, **filters
                 )
@@ -145,4 +145,21 @@ def generate_reports(
                 if report_error is not None:
                     errors.append(report_error)
 
+                bootstrap_file = data.load('reports-spec-pet.yml')
+                html_report = f'sub-{subject_label}_ses-{session_label}_pet.html'
+
+                report_error = run_reports(
+                    output_dir,
+                    subject_label,
+                    run_uuid,
+                    bootstrap_file=bootstrap_file,
+                    out_filename=html_report,
+                    reportlets_dir=reportlets_dir,
+                    errorname=f'report-{run_uuid}-{subject_label}-pet.err',
+                    subject=subject_label,
+                    session=session_label,
+                )
+                if report_error is not None:
+                    errors.append(report_error)
+
     return errors

fmriprep/reports/tests/test_reports.py

@@ -23,6 +23,10 @@
                 'sub-001_ses-003_func.html',
                 'sub-001_ses-004_func.html',
                 'sub-001_ses-005_func.html',
+                'sub-001_ses-001_pet.html',
+                'sub-001_ses-003_pet.html',
+                'sub-001_ses-004_pet.html',
+                'sub-001_ses-005_pet.html',
             ],
         ),
         (4, ['sub-001.html']),
@@ -109,3 +113,30 @@ def mock_session_list(*args, **kwargs):
         assert 'One or more execution steps failed' in html_content, (
             f'The file {expected_files[0]} did not contain the reported error.'
         )
+
+
+def test_pet_report(tmp_path, monkeypatch):
+    fake_uuid = 'fake_uuid'
+
+    pet_source = data_dir / 'work/reportlets/fmriprep'
+    sub_dir = tmp_path / 'sub-01' / 'figures'
+    sub_dir.mkdir(parents=True)
+
+    shutil.copy2(pet_source / 'sub-001/figures/sub-001_desc-about_T1w.html', sub_dir / 'sub-01_desc-about_T1w.html')
+    shutil.copy2(pet_source / 'sub-001/figures/sub-001_ses-001_task-qct_dir-LR_part-mag_desc-summary_bold.html', sub_dir / 'sub-01_ses-baseline_desc-summary_pet.html')
+    shutil.copy2(pet_source / 'sub-001/figures/sub-001_ses-001_task-qct_dir-LR_part-mag_desc-validation_bold.html', sub_dir / 'sub-01_ses-baseline_desc-validation_pet.html')
+    shutil.copy2(pet_source / 'sub-001/figures/sub-001_ses-001_task-qct_dir-LR_part-mag_desc-carpetplot_bold.svg', sub_dir / 'sub-01_ses-baseline_desc-carpetplot_pet.svg')
+    shutil.copy2(pet_source / 'sub-001/figures/sub-001_ses-001_task-qct_dir-LR_part-mag_desc-confoundcorr_bold.svg', sub_dir / 'sub-01_ses-baseline_desc-confoundcorr_pet.svg')
+    shutil.copy2(pet_source / 'sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_bbr.svg', sub_dir / 'sub-01_ses-baseline_pet.svg')
+
+    config.execution.aggr_ses_reports = 4
+    config.execution.layout = BIDSLayout(data_dir / 'pet')
+    monkeypatch.setattr(config.execution, 'bids_filters', {'pet': {'session': ['baseline']}})
+
+    failed_reports = generate_reports(['01'], tmp_path, fake_uuid)
+
+    assert not failed_reports
+    html_file = tmp_path / 'sub-01.html'
+    assert html_file.is_file()
+    html_content = html_file.read_text()
+    assert '<div id="PET"' in html_content