WIP: Add atlas support

petprep/__init__.py

@@ -26,3 +26,15 @@
     from ._version import __version__
 except ImportError:
     __version__ = '0+unknown'
+
+# Ensure niworkflows recognizes the SUIT template.
+try:  # pragma: no cover - if niworkflows is unavailable, skip patching
+    from niworkflows.utils import spaces as _spaces
+
+    if 'SUIT' not in _spaces.Reference._standard_spaces:
+        _spaces.Reference._standard_spaces = (
+            *_spaces.Reference._standard_spaces,
+            'SUIT',
+        )
+except Exception:  # pragma: no cover
+    pass

petprep/cli/parser.py

@@ -554,6 +554,13 @@ def _bids_filter(value, parser):
         help='Segmentation method to use.',
     )
 
+    g_seg.add_argument(
+        '--atlas',
+        action='store',
+        default=None,
+        help='Atlas to use for segmentation instead of FreeSurfer.',
+    )
+
     g_refmask = parser.add_argument_group('Options for reference mask generation')
     g_refmask.add_argument(
         '--ref-mask-name',
@@ -727,6 +734,10 @@ 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 opts.atlas is not None:
+        config.workflow.atlas = opts.atlas
+        config.workflow.seg = None
+
     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.')

petprep/cli/tests/test_parser.py

@@ -158,6 +158,24 @@ def test_parse_args(tmp_path, minimal_bids):
     _reset_config()
 
 
+def test_atlas_overrides_seg(tmp_path, minimal_bids):
+    """Ensure --atlas sets atlas and disables segmentation."""
+    out_dir = tmp_path / 'out'
+    parse_args(
+        args=[
+            str(minimal_bids),
+            str(out_dir),
+            'participant',
+            '--skip-bids-validation',
+            '--atlas',
+            'MyAtlas',
+        ]
+    )
+    assert config.workflow.atlas == 'MyAtlas'
+    assert config.workflow.seg is None
+    _reset_config()
+
+
 def test_bids_filter_file(tmp_path, capsys):
     bids_path = tmp_path / 'data'
     out_path = tmp_path / 'out'

petprep/config.py

@@ -599,7 +599,8 @@ class workflow(_Config):
     seg = 'gtm'
     """Segmentation approach ('gtm', 'brainstem', 'thalamicNuclei',
     'hippocampusAmygdala', 'wm', 'raphe', 'limbic')."""
-
+    atlas: str | None = None
+    """Atlas defining regional segmentation. If set, FreeSurfer segmentation is skipped."""
     pvc_tool: str | None = None
     """Tool used for partial volume correction."""
     pvc_method: str | None = None