Update to main branch

petprep/cli/parser.py

@@ -188,8 +188,13 @@ def _bids_filter(value, parser):
         'identifier (the sub- prefix can be removed)',
     )
     # Re-enable when option is actually implemented
-    # g_bids.add_argument('-s', '--session-id', action='store', default='single_session',
-    #                     help='Select a specific session to be processed')
+    g_bids.add_argument(
+        '--session-label',
+        nargs='+',
+        type=lambda label: label.removeprefix('ses-'),
+        help='A space delimited list of session identifiers or a single '
+        'identifier (the ses- prefix can be removed)',
+    )
     # Re-enable when option is actually implemented
     # g_bids.add_argument('-r', '--run-id', action='store', default='single_run',
     #                     help='Select a specific run to be processed')
@@ -749,6 +754,13 @@ def parse_args(args=None, namespace=None):
     config.execution.log_level = int(max(25 - 5 * opts.verbose_count, logging.DEBUG))
     config.from_dict(vars(opts), init=['nipype'])
 
+    if config.execution.session_label:
+        config.execution.bids_filters = config.execution.bids_filters or {}
+        config.execution.bids_filters['pet'] = {
+            **config.execution.bids_filters.get('pet', {}),
+            'session': config.execution.session_label,
+        }
+
     pvc_vals = (opts.pvc_tool, opts.pvc_method, opts.pvc_psf)
     if any(val is not None for val in pvc_vals) and not all(val is not None for val in pvc_vals):
         parser.error('Options --pvc-tool, --pvc-method and --pvc-psf must be used together.')
@@ -908,5 +920,16 @@ def parse_args(args=None, namespace=None):
             f'One or more participant labels were not found in the BIDS directory: {", ".join(missing_subjects)}.'
         )
 
+    if config.execution.session_label:
+        available_sessions = set(
+            config.execution.layout.get_sessions(subject=list(participant_label) or None)
+        )
+        missing_sessions = set(config.execution.session_label) - available_sessions
+        if missing_sessions:
+            parser.error(
+                'One or more session labels were not found in the BIDS directory: '
+                f'{", ".join(sorted(missing_sessions))}.'
+            )
+
     config.execution.participant_label = sorted(participant_label)
     config.workflow.skull_strip_template = config.workflow.skull_strip_template[0]

petprep/cli/tests/test_parser.py

@@ -24,6 +24,8 @@
 
 from argparse import ArgumentError
 
+import nibabel as nb
+import numpy as np
 import pytest
 from packaging.version import Version
 
@@ -225,6 +227,45 @@ def test_derivatives(tmp_path):
     _reset_config()
 
 
+def test_session_label_only_filters_pet(tmp_path):
+    bids = tmp_path / 'bids'
+    out_dir = tmp_path / 'out'
+    work_dir = tmp_path / 'work'
+    bids.mkdir()
+    (bids / 'dataset_description.json').write_text('{"Name": "Test", "BIDSVersion": "1.8.0"}')
+
+    anat_path = bids / 'sub-01' / 'anat' / 'sub-01_T1w.nii.gz'
+    anat_path.parent.mkdir(parents=True, exist_ok=True)
+    nb.Nifti1Image(np.zeros((5, 5, 5)), np.eye(4)).to_filename(anat_path)
+
+    pet_path = bids / 'sub-01' / 'ses-blocked' / 'pet' / 'sub-01_ses-blocked_pet.nii.gz'
+    pet_path.parent.mkdir(parents=True, exist_ok=True)
+    nb.Nifti1Image(np.zeros((5, 5, 5, 1)), np.eye(4)).to_filename(pet_path)
+    (pet_path.with_suffix('').with_suffix('.json')).write_text(
+        '{"FrameTimesStart": [0], "FrameDuration": [1]}'
+    )
+
+    try:
+        parse_args(
+            args=[
+                str(bids),
+                str(out_dir),
+                'participant',
+                '--session-label',
+                'blocked',
+                '--skip-bids-validation',
+                '-w',
+                str(work_dir),
+            ]
+        )
+
+        filters = config.execution.bids_filters
+        assert filters.get('pet', {}).get('session') == ['blocked']
+        assert 'session' not in filters.get('anat', {})
+    finally:
+        _reset_config()
+
+
 def test_pvc_argument_handling(tmp_path, minimal_bids):
     out_dir = tmp_path / 'out'
     work_dir = tmp_path / 'work'

petprep/config.py

@@ -432,6 +432,8 @@ class execution(_Config):
     """Unique identifier of this particular run."""
     participant_label = None
     """List of participant identifiers that are to be preprocessed."""
+    session_label = None
+    """List of session identifiers that are to be preprocessed."""
     task_id = None
     """Select a particular task from all available in the dataset."""
     templateflow_home = _templateflow_home

petprep/data/reports-spec-pet.yml

@@ -6,6 +6,7 @@ sections:
   reportlets:
   - bids: {datatype: figures, desc: summary, suffix: pet}
   - bids: {datatype: figures, desc: validation, suffix: pet}
+  - bids: {datatype: figures, desc: hmc, suffix: pet}
   - bids: {datatype: figures, desc: carpetplot, suffix: pet}
   - bids: {datatype: figures, desc: confoundcorr, suffix: pet}
   - bids: {datatype: figures, desc: coreg, suffix: pet}

petprep/data/reports-spec.yml

@@ -127,6 +127,11 @@ sections:
     static: false
     subtitle: PET Summary and Carpet Plot
 
+  - bids: {datatype: figures, desc: hmc, suffix: pet}
+    caption: Animated frames before and after PET head motion correction with synchronized framewise displacement trace (keep cursor over image to restart). Below is a lineplot of the Framewise Displacement (FD) in mm per frame. Red line segments between points indicate frames where FD exceeds 3 mm, suggesting motion that may impact data quality.
+    static: false
+    subtitle: Motion correction
+
   - bids: {datatype: figures, desc: confoundcorr, suffix: pet}
     caption: |
       Left: Correlation heatmap illustrating relationships among PET-derived confound variables (e.g., motion parameters, global signal).

petprep/interfaces/__init__.py

@@ -3,6 +3,7 @@
 from niworkflows.interfaces.bids import DerivativesDataSink as _DDSink
 
 from .cifti import GeneratePetCifti
+from .motion import MotionPlot
 from .tacs import ExtractRefTAC, ExtractTACs
 
 
@@ -15,4 +16,5 @@ class DerivativesDataSink(_DDSink):
     'GeneratePetCifti',
     'ExtractTACs',
     'ExtractRefTAC',
+    'MotionPlot',
 )