Merge pull request #194 from nipreps/codex/add-petref-auto-option-for-registration

Add automatic PET reference selection

Author: mnoergaard

petprep/cli/parser.py

@@ -583,13 +583,14 @@ def _bids_filter(value, parser):
     g_hmc.add_argument(
         '--petref',
         default='template',
-        choices=['template', 'twa', 'sum', 'first5min'],
+        choices=['template', 'twa', 'sum', 'first5min', 'auto'],
         help=(
             "Strategy for generating the PET reference. 'template' uses the "
             "motion correction template, while 'twa' computes a time-weighted "
             "average, 'sum' produces a summed image of the motion-corrected "
             "series, and 'first5min' averages the early (0-5 minute) portion "
-            'of the acquisition.'
+            "of the acquisition. 'auto' evaluates multiple strategies to "
+            'select the best reference.'
         ),
     )
 
@@ -788,8 +789,8 @@ 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'])
 
-    config.workflow._petref_cli_set = '--petref' in argv
-    config.workflow._pet2anat_method_cli_set = '--pet2anat-method' in argv
+    config.workflow.petref_specified = '--petref' in argv
+    config.workflow.pet2anat_method_specified = '--pet2anat-method' in argv
 
     if config.execution.session_label:
         config.execution.bids_filters = config.execution.bids_filters or {}

petprep/config.py

@@ -561,7 +561,7 @@ class workflow(_Config):
     pet2anat_method_specified: bool = False
     """Flag indicating whether ``--pet2anat-method`` was explicitly provided."""
     petref: str = 'template'
-    """Strategy for building the PET reference (``'template'``, ``'twa'``, ``'sum'`` or ``'first5min'``)."""
+    """Strategy for building the PET reference (``'template'``, ``'twa'``, ``'sum'``, ``'first5min'`` or ``'auto'``)."""
     petref_specified: bool = False
     """Flag indicating whether ``--petref`` was explicitly provided."""
     cifti_output = None

petprep/interfaces/reports.py

@@ -252,11 +252,17 @@ class FunctionalSummaryInputSpec(TraitedSpec):
         'twa',
         'sum',
         'first5min',
+        'auto',
         mandatory=True,
         desc='PET reference generation strategy',
     )
     requested_petref_strategy = traits.Enum(
-        'template', 'twa', 'sum', 'first5min', desc='User-requested PET reference strategy'
+        'template',
+        'twa',
+        'sum',
+        'first5min',
+        'auto',
+        desc='User-requested PET reference strategy',
     )
     hmc_disabled = traits.Bool(False, desc='Head motion correction disabled')
 
@@ -295,6 +301,7 @@ def _generate_segment(self):
             'twa': 'Time-weighted average of motion-corrected series',
             'sum': 'Summed motion-corrected series',
             'first5min': 'Early (0-5 minute) average of motion-corrected series',
+            'auto': 'Automatically selected reference',
         }
         petref_strategy = reference_map.get(self.inputs.petref_strategy, 'Unknown')
         requested = getattr(self.inputs, 'requested_petref_strategy', None)