🥅 Guardrail BBR only

.pylintrc

@@ -426,7 +426,8 @@ function-naming-style=snake_case
 #function-rgx=
 
 # Good variable names which should always be accepted, separated by a comma.
-good-names=c,
+good-names=by,
+           c,
            e,
            f,
            i,

CHANGELOG.md

@@ -21,6 +21,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Added the ability to run AFNI 3dDespike on template-space BOLD data.
 - Added the ability to ingress TotalReadoutTime from epi field map meta-data from the JSON sidecars.
 - Added the ability to use TotalReadoutTime of epi field maps in the calculation of FSL topup distortion correction.
+- Added ability to set minimum quality measure thresholds to boundary-based registration.
 - Difference method (``-``) for ``CPAC.utils.configuration.Configuration`` instances
 - Calculate reho and alff when timeseries in template space
 

CPAC/pipeline/cpac_pipeline.py

@@ -32,6 +32,7 @@
 from CPAC.pipeline import nipype_pipeline_engine as pe
 from CPAC.pipeline.nipype_pipeline_engine.plugins import \
     LegacyMultiProcPlugin, MultiProcPlugin
+from CPAC.qc.globals import registration_guardrails
 from nipype import config, logging
 
 from indi_aws import aws_utils, fetch_creds
@@ -199,7 +200,7 @@
     network_centrality
 )
 
-from CPAC.pipeline.random_state import set_up_random_state_logger
+from CPAC.pipeline.random_state.seed import set_up_random_state_logger
 from CPAC.pipeline.schema import valid_options
 from CPAC.utils.trimmer import the_trimmer
 from CPAC.utils import Configuration, set_subject
@@ -767,8 +768,10 @@ def initialize_nipype_wf(cfg, sub_data_dct, name=""):
     if name:
         name = f'_{name}'
 
-    workflow_name = f'cpac{name}_{sub_data_dct["subject_id"]}_{sub_data_dct["unique_id"]}'
+    workflow_name = (f'cpac{name}_{sub_data_dct["subject_id"]}_'
+                     f'{sub_data_dct["unique_id"]}')
     wf = pe.Workflow(name=workflow_name)
+    registration_guardrails.update(cfg['registration_workflows', 'guardrails'])
     wf.base_dir = cfg.pipeline_setup['working_directory']['path']
     wf.config['execution'] = {
         'hash_method': 'timestamp',

CPAC/pipeline/nipype_pipeline_engine/__init__.py

@@ -1,35 +1,35 @@
-'''Module to import Nipype Pipeline engine and override some Classes.
-See https://fcp-indi.github.io/docs/developer/nodes
-for C-PAC-specific documentation.
-See https://nipype.readthedocs.io/en/latest/api/generated/nipype.pipeline.engine.html
-for Nipype's documentation.
-
-Copyright (C) 2022  C-PAC Developers
+# Copyright (C) 2022  C-PAC Developers
 
-This file is part of C-PAC.
+# This file is part of C-PAC.
 
-C-PAC is free software: you can redistribute it and/or modify it under
-the terms of the GNU Lesser General Public License as published by the
-Free Software Foundation, either version 3 of the License, or (at your
-option) any later version.
+# C-PAC is free software: you can redistribute it and/or modify it under
+# the terms of the GNU Lesser General Public License as published by the
+# Free Software Foundation, either version 3 of the License, or (at your
+# option) any later version.
 
-C-PAC is distributed in the hope that it will be useful, but WITHOUT
-ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
-FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
-License for more details.
+# C-PAC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
+# License for more details.
 
-You should have received a copy of the GNU Lesser General Public
-License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.'''  # noqa: E501
+# You should have received a copy of the GNU Lesser General Public
+# License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
+'''Module to import Nipype Pipeline engine and override some Classes.
+See https://fcp-indi.github.io/docs/developer/nodes
+for C-PAC-specific documentation.
+See https://nipype.readthedocs.io/en/latest/api/generated/nipype.pipeline.engine.html
+for Nipype's documentation.'''  # noqa: E501  # pylint: disable=line-too-long
 from nipype.pipeline import engine as pe
 # import everything in nipype.pipeline.engine.__all__
 from nipype.pipeline.engine import *  # noqa: F401,F403
 # import our DEFAULT_MEM_GB and override Node, MapNode
 from .engine import DEFAULT_MEM_GB, get_data_size, Node, MapNode, \
-                    UNDEFINED_SIZE, Workflow
+                    registration_guardrail_node, UNDEFINED_SIZE, \
+                    Workflow
 
 __all__ = [
     interface for interface in dir(pe) if not interface.startswith('_')
-] + ['DEFAULT_MEM_GB', 'get_data_size', 'Node', 'MapNode', 'UNDEFINED_SIZE',
-     'Workflow']
+] + ['DEFAULT_MEM_GB', 'get_data_size', 'Node', 'MapNode',
+     'registration_guardrail_node', 'UNDEFINED_SIZE', 'Workflow']
 
 del pe