🐛 "regressors" → "desc-confounds_timeseries"

Author: shnizzedy

CPAC/_entrypoints/run.py

@@ -1,5 +1,5 @@
 #!/usr/bin/env python
-# Copyright (C) 2018-2024  C-PAC Developers
+# Copyright (C) 2018-2025  C-PAC Developers
 
 # This file is part of C-PAC.
 
@@ -729,16 +729,6 @@ def run_main():
                 args.fail_fast
             )
 
-        if c["pipeline_setup"]["output_directory"]["quality_control"][
-            "generate_xcpqc_files"
-        ]:
-            c["functional_preproc"]["motion_estimates_and_correction"][
-                "motion_estimates"
-            ]["calculate_motion_first"] = True
-            c["functional_preproc"]["motion_estimates_and_correction"][
-                "motion_estimates"
-            ]["calculate_motion_after"] = True
-
         if args.participant_label:
             WFLOGGER.info(
                 "#### Running C-PAC for %s", ", ".join(args.participant_label)

CPAC/func_preproc/func_motion.py

@@ -751,9 +751,7 @@ def motion_correct_mcflirt(wf, cfg, strat_pool, pipe_num):
 }
 
 
-def motion_correct_connections(
-    wf, cfg, strat_pool, pipe_num, opt
-):  # -> tuple[Any, dict[str, tuple[Node, str]]]:
+def motion_correct_connections(wf, cfg, strat_pool, pipe_num, opt):
     """Check opt for valid option, then connect that option."""
     motion_correct_options = valid_options["motion_correction"]
     if opt not in motion_correct_options:

CPAC/pipeline/engine.py

@@ -14,6 +14,8 @@
 
 # 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/>.
+"""C-PAC pipeline engine."""
+
 import ast
 import copy
 import hashlib
@@ -307,7 +309,7 @@ def regressor_dct(self, cfg) -> dict:
             "ingress_regressors."
         )
         _nr = cfg["nuisance_corrections", "2-nuisance_regression"]
-        if not hasattr(self, "timeseries"):
+        if not hasattr(self, "desc-confounds_timeseries"):
             if _nr["Regressors"]:
                 self.regressors = {reg["Name"]: reg for reg in _nr["Regressors"]}
             else:

CPAC/qc/pipeline.py

@@ -1,3 +1,21 @@
+# Copyright (C) 2018-2025  C-PAC Developers
+
+# 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 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/>.
+"""C-PAC quality control pipeline."""
+
 import pkg_resources as p
 
 from CPAC.pipeline import nipype_pipeline_engine as pe
@@ -156,7 +174,7 @@ def qc_brain_extraction(wf, cfg, strat_pool, pipe_num, opt=None):
 
 
 @nodeblock(
-    name="qc_brain_extraction",
+    name="qc_T1w_standard",
     config=["pipeline_setup", "output_directory", "quality_control"],
     switch=["generate_quality_control_images"],
     inputs=["space-template_desc-preproc_T1w", "T1w-brain-template"],

CPAC/qc/xcp.py

@@ -1,3 +1,19 @@
+# Copyright (C) 2021-2025  C-PAC Developers
+
+# 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 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/>.
 """
 Generate XCP-stype quality control files.
 
@@ -439,7 +455,7 @@ def get_entity_part(key):
             "space-bold_desc-brain_mask",
             ["T1w-brain-template-mask", "EPI-template-mask"],
             ["space-template_desc-bold_mask", "space-EPItemplate_desc-bold_mask"],
-            "regressors",
+            "desc-confounds_timeseries",
             ["T1w-brain-template-funcreg", "EPI-brain-template-funcreg"],
             [
                 "desc-movementParametersUnfiltered_motion",
@@ -458,7 +474,7 @@ def qc_xcp(wf, cfg, strat_pool, pipe_num, opt=None):
     # pylint: disable=invalid-name, unused-argument
     if cfg[
         "nuisance_corrections", "2-nuisance_regression", "run"
-    ] and not strat_pool.check_rpool("regressors"):
+    ] and not strat_pool.check_rpool("desc-confounds_timeseries"):
         return wf, {}
     bids_info = pe.Node(
         Function(
@@ -501,8 +517,8 @@ def qc_xcp(wf, cfg, strat_pool, pipe_num, opt=None):
     )
     qc_file.inputs.desc = "preproc"
     qc_file.inputs.regressors = (
-        strat_pool.node_data("regressors")
-        .node.name.split("regressors_")[-1][::-1]
+        strat_pool.node_data("desc-confounds_timeseries")
+        .node.name.split("desc-confounds_timeseries_")[-1][::-1]
         .split("_", 1)[-1][::-1]
     )
     bold_to_T1w_mask = pe.Node(