🔀 Merge branch 'develop' into 'decrease-fragility/xcpqc'

Author: shnizzedy

.dockerignore

@@ -4,5 +4,6 @@ cpac_runs
 .env*
 .git
 .github
+!.github/CODEOWNERS
 !.github/scripts
 *.tar.gz

.github/CODEOWNERS

@@ -0,0 +1,30 @@
+# Copyright (C) 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/>.
+
+# Global maintenance
+*                 @FCP-INDI/Maintenance
+
+# DevOps
+/pyproject.toml   @FCP-INDI/DevOps
+/requirements.txt @FCP-INDI/DevOps
+/setup.py         @FCP-INDI/DevOps
+/dev              @FCP-INDI/DevOps
+/scripts          @FCP-INDI/DevOps
+/.*               @FCP-INDI/DevOps
+/.circleci        @FCP-INDI/DevOps
+/.github          @FCP-INDI/DevOps
+**/*Dockerfile    @FCP-INDI/DevOps

CHANGELOG.md

@@ -57,6 +57,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   - Removed broken support for native-space masking.
   - Introduced a new `template_space_func_masking` section in the pipeline config for template-space-only methods.
   - Moved `Anatomical_Resampled` masking method from `func_masking` to the `template_space_func_masking`.
+- Turned `On` boundary_based_registration for abcd-options preconfig.
+- Refactored `transform_timeseries_to_T1template_abcd` nodeblock removing unnecessary nodes, changing `desc-preproc_T1w` inputs as reference to `desc-head_T1w`.
+- Appended `T1w to Template` FOV match transform to the XFM.
 
 ### Upgraded
 

CPAC/func_preproc/func_preproc.py

@@ -1559,12 +1559,12 @@ def anat_brain_to_bold_res(wf_name, cfg, pipe_num):
 
     inputNode = pe.Node(
         util.IdentityInterface(
-            fields=["T1w-template-funcreg", "space-template_desc-preproc_T1w"]
+            fields=["T1w-template-funcreg", "space-template_desc-head_T1w"]
         ),
         name="inputspec",
     )
     outputNode = pe.Node(
-        util.IdentityInterface(fields=["space-template_res-bold_desc-brain_T1w"]),
+        util.IdentityInterface(fields=["space-template_res-bold_desc-head_T1w"]),
         name="outputspec",
     )
 
@@ -1579,15 +1579,15 @@ def anat_brain_to_bold_res(wf_name, cfg, pipe_num):
     ]["registration"]["FSL-FNIRT"]["identity_matrix"]
 
     wf.connect(
-        inputNode, "space-template_desc-preproc_T1w", anat_brain_to_func_res, "in_file"
+        inputNode, "space-template_desc-head_T1w", anat_brain_to_func_res, "in_file"
     )
     wf.connect(inputNode, "T1w-template-funcreg", anat_brain_to_func_res, "ref_file")
 
     wf.connect(
         anat_brain_to_func_res,
         "out_file",
         outputNode,
-        "space-template_res-bold_desc-brain_T1w",
+        "space-template_res-bold_desc-head_T1w",
     )
     return wf
 
@@ -1598,7 +1598,7 @@ def anat_brain_mask_to_bold_res(wf_name, cfg, pipe_num):
     wf = pe.Workflow(name=f"{wf_name}_{pipe_num}")
     inputNode = pe.Node(
         util.IdentityInterface(
-            fields=["space-template_desc-brain_mask", "space-template_desc-preproc_T1w"]
+            fields=["space-template_desc-brain_mask", "space-template_desc-head_T1w"]
         ),
         name="inputspec",
     )
@@ -1625,7 +1625,7 @@ def anat_brain_mask_to_bold_res(wf_name, cfg, pipe_num):
     )
     wf.connect(
         inputNode,
-        "space-template_desc-preproc_T1w",
+        "space-template_desc-head_T1w",
         anat_brain_mask_to_func_res,
         "ref_file",
     )
@@ -1649,11 +1649,11 @@ def anat_brain_mask_to_bold_res(wf_name, cfg, pipe_num):
     option_val="Anatomical_Resampled",
     inputs=[
         "T1w-template-funcreg",
-        "space-template_desc-preproc_T1w",
+        "space-template_desc-head_T1w",
         "space-template_desc-brain_mask",
     ],
     outputs=[
-        "space-template_res-bold_desc-brain_T1w",
+        "space-template_res-bold_desc-head_T1w",
         "space-template_desc-bold_mask",
     ],
 )
@@ -1666,9 +1666,9 @@ def bold_mask_anatomical_resampled(wf, cfg, strat_pool, pipe_num, opt=None):
         wf_name="anat_brain_to_bold_res", cfg=cfg, pipe_num=pipe_num
     )
 
-    node, out = strat_pool.get_data("space-template_desc-preproc_T1w")
+    node, out = strat_pool.get_data("space-template_desc-head_T1w")
     wf.connect(
-        node, out, anat_brain_to_func_res, "inputspec.space-template_desc-preproc_T1w"
+        node, out, anat_brain_to_func_res, "inputspec.space-template_desc-head_T1w"
     )
 
     node, out = strat_pool.get_data("T1w-template-funcreg")
@@ -1690,15 +1690,15 @@ def bold_mask_anatomical_resampled(wf, cfg, strat_pool, pipe_num, opt=None):
 
     wf.connect(
         anat_brain_to_func_res,
-        "outputspec.space-template_res-bold_desc-brain_T1w",
+        "outputspec.space-template_res-bold_desc-head_T1w",
         anat_brain_mask_to_func_res,
-        "inputspec.space-template_desc-preproc_T1w",
+        "inputspec.space-template_desc-head_T1w",
     )
 
     outputs = {
-        "space-template_res-bold_desc-brain_T1w": (
+        "space-template_res-bold_desc-head_T1w": (
             anat_brain_to_func_res,
-            "outputspec.space-template_res-bold_desc-brain_T1w",
+            "outputspec.space-template_res-bold_desc-head_T1w",
         ),
         "space-template_desc-bold_mask": (
             anat_brain_mask_to_func_res,
@@ -1896,7 +1896,7 @@ def bold_masking(wf, cfg, strat_pool, pipe_num, opt=None):
         ["functional_preproc", "template_space_func_masking", "run"],
     ],
     inputs=[
-        ("space-template_desc-preproc_bold", "space-template_desc-bold_mask"),
+        ("space-template_desc-head_bold", "space-template_desc-bold_mask"),
     ],
     outputs={
         "space-template_desc-preproc_bold": {
@@ -1907,10 +1907,6 @@ def bold_masking(wf, cfg, strat_pool, pipe_num, opt=None):
             "Description": "The skull-stripped BOLD time-series.",
             "SkullStripped": True,
         },
-        "space-template_desc-head_bold": {
-            "Description": "The non skull-stripped BOLD time-series.",
-            "SkullStripped": False,
-        },
     },
 )
 def template_space_bold_masking(
@@ -1929,9 +1925,7 @@ def template_space_bold_masking(
     func_apply_mask.inputs.expr = "a*b"
     func_apply_mask.inputs.outputtype = "NIFTI_GZ"
 
-    node_head_bold, out_head_bold = strat_pool.get_data(
-        "space-template_desc-preproc_bold"
-    )
+    node_head_bold, out_head_bold = strat_pool.get_data("space-template_desc-head_bold")
     wf.connect(node_head_bold, out_head_bold, func_apply_mask, "in_file_a")
 
     node, out = strat_pool.get_data("space-template_desc-bold_mask")
@@ -1940,7 +1934,6 @@ def template_space_bold_masking(
     outputs: POOL_RESOURCE_DICT = {
         "space-template_desc-preproc_bold": (func_apply_mask, "out_file"),
         "space-template_desc-brain_bold": (func_apply_mask, "out_file"),
-        "space-template_desc-head_bold": (node_head_bold, out_head_bold),
     }
 
     return wf, outputs

CPAC/pipeline/cpac_pipeline.py

@@ -1301,6 +1301,13 @@ def build_workflow(subject_id, sub_dict, cfg, pipeline_name=None):
 
         pipeline_blocks += stack_motion_blocks(func_blocks, cfg, rpool)
 
+    # Template space functional mask
+    if cfg.functional_preproc["template_space_func_masking"]["run"]:
+        if not rpool.check_rpool("space-template_desc-bold_mask"):
+            pipeline_blocks += [
+                bold_mask_anatomical_resampled,
+            ]
+
     # BOLD to T1 coregistration
     if cfg.registration_workflows["functional_registration"]["coregistration"][
         "run"
@@ -1460,13 +1467,8 @@ def build_workflow(subject_id, sub_dict, cfg, pipeline_name=None):
             warp_deriv_mask_to_EPItemplate,
         ]
 
-    # Template space functional masking
+    # Apply mask in template space
     if cfg.functional_preproc["template_space_func_masking"]["run"]:
-        if not rpool.check_rpool("space-template_desc-bold_mask"):
-            pipeline_blocks += [
-                bold_mask_anatomical_resampled,
-            ]
-
         pipeline_blocks += [
             template_space_bold_masking,
         ]

CPAC/pipeline/schema.py

@@ -845,10 +845,10 @@ def sanitize(filename):
                     },
                     "boundary_based_registration": {
                         "run": forkable,
+                        "reference": In({"whole-head", "brain"}),
                         "bbr_schedule": str,
                         "bbr_wm_map": In({"probability_map", "partial_volume_map"}),
                         "bbr_wm_mask_args": str,
-                        "reference": In({"whole-head", "brain"}),
                     },
                 },
                 "EPI_registration": {