FCP-INDI · shnizzedy · Nov 13, 2024 · Nov 13, 2024 · Nov 13, 2024 · Nov 14, 2024
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -29,6 +29,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - New switch `mask_sbref` under `func_input_prep` in functional registration and set to default `on`.
 - New resource `desc-head_bold` as non skull-stripped bold from nodeblock `bold_masking`.
 - `censor_file_path` from `offending_timepoints_connector` in the `build_nuisance_regressor` node.
+- `mri_robust_template` for longitudinal template generation.
+- `max_iter` parameter for longitudinal template generation.
 
 ### Changed
 
@@ -45,6 +47,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Input `desc-brain_bold` to `desc-preproc_bold` for `sbref` generation nodeblock `coregistration_prep_vol`.
 - Turned `generate_xcpqc_files` on for all preconfigurations except `blank`.
 - Introduced specific switch `restore_t1w_intensity` for `correct_restore_brain_intensity_abcd` nodeblock, enabling it by default only in `abcd-options` pre-config.
+- Updated GitHub Actions to run automated integration and regression tests on HPC.
+- Made `mri_robust_template` default implementation for longitudinal template generation.
 
 ### Fixed
 
@@ -54,6 +58,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - A bug in which bandpass filters always assumed 1D regressor files have exactly 5 header rows.
 - Removed an erroneous connection to AFNI 3dTProject in nuisance denoising that would unnecessarily send a spike regressor as a censor. This would sometimes cause TRs to unnecessarily be dropped from the timeseries as if scrubbing were being performed.
 - Supplied missing `subject_id` for longitudinal workflow logger and make that field optional for the logger.
+- Lingering calls to `cpac_outputs.csv` (was changed to `cpac_outputs.tsv` in v1.8.1).
+- A bug in the `freesurfer_abcd_preproc` nodeblock where the `Template` image was incorrectly used as `reference` during the `inverse_warp` step. Replacing it with the subject-specific `T1w` image resolved the issue of the `desc-restoreBrain_T1w` being chipped off.
+- A bug in `ideal_bandpass` where the frequency mask was incorrectly applied, which caused filter to fail in certain cases.
 
 ### Removed
 

diff --git a/CPAC/alff/alff.py b/CPAC/alff/alff.py
@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# Copyright (C) 2012-2024  C-PAC Developers
+# Copyright (C) 2012-2025  C-PAC Developers
 
 # This file is part of C-PAC.
 
@@ -23,9 +23,8 @@
 from CPAC.alff.utils import get_opt_string
 from CPAC.pipeline import nipype_pipeline_engine as pe
 from CPAC.pipeline.nodeblock import nodeblock
-from CPAC.registration.registration import apply_transform
+from CPAC.registration.utils import apply_transform
 from CPAC.utils.interfaces import Function
-from CPAC.utils.utils import check_prov_for_regtool
 
 
 def create_alff(wf_name="alff_workflow"):
@@ -320,10 +319,7 @@ def alff_falff(wf, cfg, strat_pool, pipe_num, opt=None):
 def alff_falff_space_template(wf, cfg, strat_pool, pipe_num, opt=None):
     outputs = {}
     if strat_pool.check_rpool("desc-denoisedNofilt_bold"):
-        xfm_prov = strat_pool.get_cpac_provenance(
-            "from-bold_to-template_mode-image_xfm"
-        )
-        reg_tool = check_prov_for_regtool(xfm_prov)
+        reg_tool = strat_pool.reg_tool("from-bold_to-template_mode-image_xfm")
 
         num_cpus = cfg.pipeline_setup["system_config"]["max_cores_per_participant"]
 

diff --git a/CPAC/anat_preproc/anat_preproc.py b/CPAC/anat_preproc/anat_preproc.py
@@ -34,7 +34,7 @@
     wb_command,
 )
 from CPAC.pipeline import nipype_pipeline_engine as pe
-from CPAC.pipeline.nodeblock import nodeblock
+from CPAC.pipeline.nodeblock import nodeblock, NODEBLOCK_RETURN
 from CPAC.utils.interfaces import Function
 from CPAC.utils.interfaces.fsl import Merge as fslMerge
 
@@ -1227,15 +1227,7 @@ def freesurfer_fsl_brain_connector(wf, cfg, strat_pool, pipe_num, opt):
     wf.connect(node, out, convert_fs_T1_to_nifti, "in_file")
 
     # 3dresample -orient RPI -inset brainmask.nii.gz -prefix brain_fs.nii.gz
-    reorient_fs_brainmask = pe.Node(
-        interface=afni.Resample(),
-        name=f"reorient_fs_brainmask_{node_id}",
-        mem_gb=0,
-        mem_x=(0.0115, "in_file", "t"),
-    )
-    reorient_fs_brainmask.inputs.orientation = cfg.pipeline_setup["desired_orientation"]
-    reorient_fs_brainmask.inputs.outputtype = "NIFTI_GZ"
-
+    reorient_fs_brainmask = cfg.orientation_node(f"reorient_fs_brainmask_{node_id}")
     wf.connect(
         convert_fs_brainmask_to_nifti, "out_file", reorient_fs_brainmask, "in_file"
     )
@@ -1249,15 +1241,7 @@ def freesurfer_fsl_brain_connector(wf, cfg, strat_pool, pipe_num, opt):
     wf.connect(reorient_fs_brainmask, "out_file", binarize_fs_brain, "in_file")
 
     # 3dresample -orient RPI -inset T1.nii.gz -prefix head_fs.nii.gz
-    reorient_fs_T1 = pe.Node(
-        interface=afni.Resample(),
-        name=f"reorient_fs_T1_{node_id}",
-        mem_gb=0,
-        mem_x=(0.0115, "in_file", "t"),
-    )
-    reorient_fs_T1.inputs.orientation = cfg.pipeline_setup["desired_orientation"]
-    reorient_fs_T1.inputs.outputtype = "NIFTI_GZ"
-
+    reorient_fs_T1 = cfg.orientation_node(f"reorient_fs_T1_{node_id}")
     wf.connect(convert_fs_T1_to_nifti, "out_file", reorient_fs_T1, "in_file")
 
     # flirt -in head_fs.nii.gz -ref ${FSLDIR}/data/standard/MNI152_T1_1mm.nii.gz \
@@ -1447,22 +1431,14 @@ def mask_T2(wf_name="mask_T2"):
     inputs=["T1w"],
     outputs=["desc-preproc_T1w", "desc-reorient_T1w", "desc-head_T1w"],
 )
-def anatomical_init(wf, cfg, strat_pool, pipe_num, opt=None):
+def anatomical_init(wf, cfg, strat_pool, pipe_num, opt=None) -> NODEBLOCK_RETURN:
     anat_deoblique = pe.Node(interface=afni.Refit(), name=f"anat_deoblique_{pipe_num}")
     anat_deoblique.inputs.deoblique = True
 
     node, out = strat_pool.get_data("T1w")
     wf.connect(node, out, anat_deoblique, "in_file")
 
-    anat_reorient = pe.Node(
-        interface=afni.Resample(),
-        name=f"anat_reorient_{pipe_num}",
-        mem_gb=0,
-        mem_x=(0.0115, "in_file", "t"),
-    )
-    anat_reorient.inputs.orientation = cfg.pipeline_setup["desired_orientation"]
-    anat_reorient.inputs.outputtype = "NIFTI_GZ"
-
+    anat_reorient = cfg.orientation_node(f"anat_reorient_{pipe_num}")
     wf.connect(anat_deoblique, "out_file", anat_reorient, "in_file")
 
     outputs = {
@@ -2262,15 +2238,7 @@ def anatomical_init_T2(wf, cfg, strat_pool, pipe_num, opt=None):
     node, out = strat_pool.get_data("T2w")
     wf.connect(node, out, T2_deoblique, "in_file")
 
-    T2_reorient = pe.Node(
-        interface=afni.Resample(),
-        name=f"T2_reorient_{pipe_num}",
-        mem_gb=0,
-        mem_x=(0.0115, "in_file", "t"),
-    )
-    T2_reorient.inputs.orientation = cfg.pipeline_setup["desired_orientation"]
-    T2_reorient.inputs.outputtype = "NIFTI_GZ"
-
+    T2_reorient = cfg.orientation_node(f"T2_reorient_{pipe_num}")
     wf.connect(T2_deoblique, "out_file", T2_reorient, "in_file")
 
     outputs = {

diff --git a/CPAC/anat_preproc/lesion_preproc.py b/CPAC/anat_preproc/lesion_preproc.py
@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# Copyright (C) 2019-2023  C-PAC Developers
+# Copyright (C) 2019-2025  C-PAC Developers
 
 # This file is part of C-PAC.
 
@@ -20,6 +20,7 @@
 
 from CPAC.pipeline import nipype_pipeline_engine as pe
 from CPAC.utils.interfaces import Function
+from CPAC.utils.nifti_utils import orientation_node
 
 
 def inverse_lesion(lesion_path):
@@ -126,18 +127,10 @@ def create_lesion_preproc(cfg=None, wf_name="lesion_preproc"):
     preproc.connect(lesion_deoblique, "out_file", outputnode, "refit")
 
     # Anatomical reorientation
-    lesion_reorient = pe.Node(
-        interface=afni.Resample(),
-        name="lesion_reorient",
-        mem_gb=0,
-        mem_x=(0.0115, "in_file", "t"),
+    node_name = "lesion_reorient"
+    lesion_reorient = (
+        cfg.orientation_node(node_name) if cfg else orientation_node(node_name, "RPI")
     )
-
-    lesion_reorient.inputs.orientation = (
-        cfg.pipeline_setup["desired_orientation"] if cfg else "RPI"
-    )
-    lesion_reorient.inputs.outputtype = "NIFTI_GZ"
-
     preproc.connect(lesion_deoblique, "out_file", lesion_reorient, "in_file")
     preproc.connect(lesion_reorient, "out_file", outputnode, "reorient")
 

diff --git a/CPAC/func_preproc/func_motion.py b/CPAC/func_preproc/func_motion.py
@@ -1,4 +1,4 @@
-# Copyright (C) 2012-2024  C-PAC Developers
+# Copyright (C) 2012-2025  C-PAC Developers
 
 # This file is part of C-PAC.
 
@@ -34,7 +34,6 @@
 from CPAC.pipeline.nodeblock import nodeblock
 from CPAC.pipeline.schema import valid_options
 from CPAC.utils.interfaces.function import Function
-from CPAC.utils.utils import check_prov_for_motion_tool
 
 
 @nodeblock(
@@ -68,8 +67,7 @@
 )
 def calc_motion_stats(wf, cfg, strat_pool, pipe_num, opt=None):
     """Calculate motion statistics for motion parameters."""
-    motion_prov = strat_pool.get_cpac_provenance("desc-movementParameters_motion")
-    motion_correct_tool = check_prov_for_motion_tool(motion_prov)
+    motion_correct_tool = strat_pool.motion_tool("desc-movementParameters_motion")
     coordinate_transformation = [
         "filtered-coordinate-transformation",
         "coordinate-transformation",

diff --git a/CPAC/func_preproc/func_preproc.py b/CPAC/func_preproc/func_preproc.py
@@ -1,4 +1,4 @@
-# Copyright (C) 2012-2023  C-PAC Developers
+# Copyright (C) 2012-2025  C-PAC Developers
 
 # This file is part of C-PAC.
 
@@ -718,16 +718,7 @@ def func_reorient(wf, cfg, strat_pool, pipe_num, opt=None):
     node, out = strat_pool.get_data("bold")
     wf.connect(node, out, func_deoblique, "in_file")
 
-    func_reorient = pe.Node(
-        interface=afni_utils.Resample(),
-        name=f"func_reorient_{pipe_num}",
-        mem_gb=0,
-        mem_x=(0.0115, "in_file", "t"),
-    )
-
-    func_reorient.inputs.orientation = cfg.pipeline_setup["desired_orientation"]
-    func_reorient.inputs.outputtype = "NIFTI_GZ"
-
+    func_reorient = cfg.orientation_node(f"func_reorient_{pipe_num}")
     wf.connect(func_deoblique, "out_file", func_reorient, "in_file")
 
     outputs = {
@@ -1320,16 +1311,7 @@ def bold_mask_anatomical_refined(wf, cfg, strat_pool, pipe_num, opt=None):
     node, out = strat_pool.get_data("bold")
     wf.connect(node, out, func_deoblique, "in_file")
 
-    func_reorient = pe.Node(
-        interface=afni_utils.Resample(),
-        name=f"raw_func_reorient_{pipe_num}",
-        mem_gb=0,
-        mem_x=(0.0115, "in_file", "t"),
-    )
-
-    func_reorient.inputs.orientation = cfg.pipeline_setup["desired_orientation"]
-    func_reorient.inputs.outputtype = "NIFTI_GZ"
-
+    func_reorient = cfg.orientation_node(f"raw_func_reorient_{pipe_num}")
     wf.connect(func_deoblique, "out_file", func_reorient, "in_file")
 
     wf.connect(func_reorient, "out_file", init_bold_mask, "inputspec.func")

diff --git a/CPAC/longitudinal/__init__.py b/CPAC/longitudinal/__init__.py
@@ -18,6 +18,7 @@
 
 from CPAC.utils.docs import DOCS_URL_PREFIX
 
+assert isinstance(__doc__, str)
 __doc__ += f"""
 
 See {DOCS_URL_PREFIX}/user/longitudinal