Merge branch 'develop' into fix/ccs-options-brain-masking

Author: sgiavasis

.github/Dockerfiles/base-lite.Dockerfile

@@ -52,6 +52,8 @@ COPY --from=fsl /usr/lib/x86_64-linux-gnu /usr/lib/x86_64-linux-gnu
 COPY --from=fsl /usr/bin /usr/bin
 COPY --from=fsl /usr/local/bin /usr/local/bin
 COPY --from=fsl /usr/share/fsl /usr/share/fsl
+RUN apt-get update \
+    && apt-get install --no-install-recommends -y bc
 
 # Installing C-PAC dependencies
 COPY requirements.txt /opt/requirements.txt

.github/Dockerfiles/base-standard.Dockerfile

@@ -22,9 +22,14 @@ Standard software dependencies for C-PAC standard images"
 LABEL org.opencontainers.image.source=https://github.com/FCP-INDI/C-PAC
 USER root
 
+# Installing ANTs
+ENV LANG="en_US.UTF-8" \
+    LC_ALL="en_US.UTF-8" \
+    ANTSPATH=/usr/lib/ants/bin \
+    PATH=/usr/lib/ants/bin:$PATH
+
 # Installing FreeSurfer
 RUN apt-get update \
-    && apt-get install --no-install-recommends -y bc \
     && yes | mamba install tcsh \
     && yes | mamba clean --all \
     && cp -l `which tcsh` /bin/tcsh \

CHANGELOG.md

@@ -33,6 +33,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - `deoblique` field in pipeline config with `warp` and `refit` options to apply `3dWarp` or `3drefit` during data initialization.
 - `organism` configuration option.
 - Functionality to convert `space-T1w_desc-loose_brain_mask` and `space-T1w_desc-tight_brain_mask` into generic brain mask `space-T1w_desc-brain_mask` to use in brain extraction nodeblock downstream.
+- `desc-ABCDpreproc_T1w` to the outputs
+- `bc` to `lite` container images.
 
 ### Changed
 
@@ -70,6 +72,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - 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.
+- A bug where `$ANTSPATH` was unset in C-PAC with FreeSurfer images.
 
 ### Upgraded dependencies
 

CPAC/anat_preproc/anat_preproc.py

@@ -2189,7 +2189,6 @@ def brain_mask_acpc_freesurfer_fsl_loose(wf, cfg, strat_pool, pipe_num, opt=None
     outputs={
         "desc-preproc_T1w": {"SkullStripped": "True"},
         "desc-brain_T1w": {"SkullStripped": "True"},
-        "desc-head_T1w": {"SkullStripped": "False"},
     },
 )
 def brain_extraction(wf, cfg, strat_pool, pipe_num, opt=None):
@@ -2227,7 +2226,6 @@ def brain_extraction(wf, cfg, strat_pool, pipe_num, opt=None):
     outputs = {
         "desc-preproc_T1w": (anat_skullstrip_orig_vol, "out_file"),
         "desc-brain_T1w": (anat_skullstrip_orig_vol, "out_file"),
-        "desc-head_T1w": (node_T1w, out_T1w),
     }
 
     return (wf, outputs)

CPAC/distortion_correction/distortion_correction.py

@@ -36,7 +36,7 @@
 from CPAC.pipeline import nipype_pipeline_engine as pe
 from CPAC.pipeline.nodeblock import nodeblock
 from CPAC.utils import function
-from CPAC.utils.datasource import match_epi_fmaps
+from CPAC.utils.datasource import match_epi_fmaps_function_node
 from CPAC.utils.interfaces.function import Function
 
 
@@ -406,23 +406,7 @@ def distcor_blip_afni_qwarp(wf, cfg, strat_pool, pipe_num, opt=None):
            3dQWarp. The output of this can then proceed to
            func_preproc.
     """
-    match_epi_imports = ["import json"]
-    match_epi_fmaps_node = pe.Node(
-        Function(
-            input_names=[
-                "bold_pedir",
-                "epi_fmap_one",
-                "epi_fmap_params_one",
-                "epi_fmap_two",
-                "epi_fmap_params_two",
-            ],
-            output_names=["opposite_pe_epi", "same_pe_epi"],
-            function=match_epi_fmaps,
-            imports=match_epi_imports,
-            as_module=True,
-        ),
-        name=f"match_epi_fmaps_{pipe_num}",
-    )
+    match_epi_fmaps_node = match_epi_fmaps_function_node(f"match_epi_fmaps_{pipe_num}")
 
     node, out = strat_pool.get_data("epi-1")
     wf.connect(node, out, match_epi_fmaps_node, "epi_fmap_one")

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.
 
@@ -16,13 +16,15 @@
 # License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
 """Functional preprocessing."""
 
+from typing import TYPE_CHECKING
+
 # pylint: disable=ungrouped-imports,wrong-import-order,wrong-import-position
 from nipype.interfaces import afni, ants, fsl, utility as util
 from nipype.interfaces.afni import preprocess, utils as afni_utils
 
 from CPAC.func_preproc.utils import get_num_slices, interpolate_slice_timing, nullify
 from CPAC.pipeline import nipype_pipeline_engine as pe
-from CPAC.pipeline.nodeblock import nodeblock
+from CPAC.pipeline.nodeblock import nodeblock, NODEBLOCK_RETURN, POOL_RESOURCE_DICT
 from CPAC.utils.interfaces import Function
 from CPAC.utils.interfaces.ants import (
     AI,  # niworkflows
@@ -31,6 +33,10 @@
 )
 from CPAC.utils.utils import add_afni_prefix, afni_3dwarp
 
+if TYPE_CHECKING:
+    from CPAC.pipeline.engine import ResourcePool
+    from CPAC.utils.configuration import Configuration
+
 
 def collect_arguments(*args):
     """Collect arguments."""
@@ -1890,7 +1896,9 @@ def bold_masking(wf, cfg, strat_pool, pipe_num, opt=None):
         ["functional_preproc", "run"],
         ["functional_preproc", "template_space_func_masking", "run"],
     ],
-    inputs=[("space-template_desc-preproc_bold", "space-template_desc-bold_mask")],
+    inputs=[
+        ("space-template_desc-preproc_bold", "space-template_desc-bold_mask"),
+    ],
     outputs={
         "space-template_desc-preproc_bold": {
             "Description": "The skull-stripped BOLD time-series.",
@@ -1906,7 +1914,13 @@ def bold_masking(wf, cfg, strat_pool, pipe_num, opt=None):
         },
     },
 )
-def template_space_bold_masking(wf, cfg, strat_pool, pipe_num, opt=None):
+def template_space_bold_masking(
+    wf: pe.Workflow,
+    cfg: "Configuration",
+    strat_pool: "ResourcePool",
+    pipe_num: int,
+    opt: None = None,
+) -> NODEBLOCK_RETURN:
     """Mask the bold in template space."""
     func_apply_mask = pe.Node(
         interface=afni_utils.Calc(),
@@ -1924,13 +1938,13 @@ def template_space_bold_masking(wf, cfg, strat_pool, pipe_num, opt=None):
     node, out = strat_pool.get_data("space-template_desc-bold_mask")
     wf.connect(node, out, func_apply_mask, "in_file_b")
 
-    outputs = {
+    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)
+    return wf, outputs
 
 
 @nodeblock(

CPAC/nuisance/nuisance.py

@@ -40,8 +40,8 @@
     TR_string_to_float,
 )
 from CPAC.pipeline import nipype_pipeline_engine as pe
-from CPAC.pipeline.engine import ResourcePool
-from CPAC.pipeline.nodeblock import nodeblock
+from CPAC.pipeline.engine import NodeData, ResourcePool
+from CPAC.pipeline.nodeblock import nodeblock, NODEBLOCK_RETURN, POOL_RESOURCE_DICT
 from CPAC.registration.registration import (
     apply_transform,
     warp_timeseries_to_EPItemplate,
@@ -2457,8 +2457,15 @@ def nuisance_regressors_generation_EPItemplate(wf, cfg, strat_pool, pipe_num, op
     inputs=[
         (
             "desc-preproc_bold",
-            "space-bold_desc-brain_mask",
+            "desc-reorient_bold",
+            "sbref",
+            [
+                "space-bold_desc-brain_mask",
+                "space-template_desc-bold_mask",
+                "space-template_desc-brain_mask",
+            ],
             "from-bold_to-T1w_mode-image_desc-linear_xfm",
+            "from-template_to-bold_mode-image_xfm",
             "desc-movementParameters_motion",
             "framewise-displacement-jenkinson",
             "framewise-displacement-power",
@@ -2486,7 +2493,13 @@ def nuisance_regressors_generation_EPItemplate(wf, cfg, strat_pool, pipe_num, op
         "lateral-ventricles-mask",
         "TR",
     ],
-    outputs=["desc-confounds_timeseries", "censor-indices"],
+    outputs={
+        "desc-confounds_timeseries": {},
+        "censor-indices": {},
+        "space-bold_desc-brain_mask": {
+            "Description": "Binary brain mask of the BOLD functional time-series, transformed from template space."
+        },
+    },
 )
 def nuisance_regressors_generation_T1w(wf, cfg, strat_pool, pipe_num, opt=None):
     return nuisance_regressors_generation(wf, cfg, strat_pool, pipe_num, opt, "T1w")
@@ -2499,38 +2512,37 @@ def nuisance_regressors_generation(
     pipe_num: int,
     opt: dict,
     space: Literal["T1w", "bold"],
-) -> tuple[Workflow, dict]:
-    """Generate nuisance regressors.
-
-    Parameters
-    ----------
-    wf : ~nipype.pipeline.engine.workflows.Workflow
-
-    cfg : ~CPAC.utils.configuration.Configuration
-
-    strat_pool : ~CPAC.pipeline.engine.ResourcePool
-
-    pipe_num : int
-
-    opt : dict
-
-    space : str
-        T1w or bold
-
-    Returns
-    -------
-    wf : nipype.pipeline.engine.workflows.Workflow
+) -> NODEBLOCK_RETURN:
+    """Generate nuisance regressors."""
+    from CPAC.nuisance.utils.xfm import transform_bold_mask_to_native
 
-    outputs : dict
-    """
     prefixes = [f"space-{space}_"] * 2
     reg_tool = None
+    outputs: POOL_RESOURCE_DICT = {}
+
+    brain_mask = (
+        strat_pool.node_data("space-bold_desc-brain_mask")
+        if strat_pool.check_rpool("space-bold_desc-brain_mask")
+        else NodeData()
+    )
     if space == "T1w":
         prefixes[0] = ""
         if strat_pool.check_rpool("from-template_to-T1w_mode-image_desc-linear_xfm"):
             reg_tool = strat_pool.reg_tool(
                 "from-template_to-T1w_mode-image_desc-linear_xfm"
             )
+            if brain_mask.node is NotImplemented:
+                if reg_tool and strat_pool.check_rpool(
+                    ["space-template_desc-bold_mask", "space-template_desc-brain_mask"]
+                ):
+                    outputs["space-bold_desc-brain_mask"] = (
+                        transform_bold_mask_to_native(
+                            wf, strat_pool, cfg, pipe_num, reg_tool
+                        )
+                    )
+                    brain_mask.node, brain_mask.out = outputs[
+                        "space-bold_desc-brain_mask"
+                    ]
     elif space == "bold":
         reg_tool = strat_pool.reg_tool(
             "from-EPItemplate_to-bold_mode-image_desc-linear_xfm"
@@ -2575,8 +2587,12 @@ def nuisance_regressors_generation(
     node, out = strat_pool.get_data("desc-preproc_bold")
     wf.connect(node, out, regressors, "inputspec.functional_file_path")
 
-    node, out = strat_pool.get_data("space-bold_desc-brain_mask")
-    wf.connect(node, out, regressors, "inputspec.functional_brain_mask_file_path")
+    wf.connect(
+        brain_mask.node,
+        brain_mask.out,
+        regressors,
+        "inputspec.functional_brain_mask_file_path",
+    )
 
     if strat_pool.check_rpool(f"desc-brain_{space}"):
         node, out = strat_pool.get_data(f"desc-brain_{space}")
@@ -2738,12 +2754,13 @@ def nuisance_regressors_generation(
     node, out = strat_pool.get_data("TR")
     wf.connect(node, out, regressors, "inputspec.tr")
 
-    outputs = {
-        "desc-confounds_timeseries": (regressors, "outputspec.regressors_file_path"),
-        "censor-indices": (regressors, "outputspec.censor_indices"),
-    }
+    outputs["desc-confounds_timeseries"] = (
+        regressors,
+        "outputspec.regressors_file_path",
+    )
+    outputs["censor-indices"] = (regressors, "outputspec.censor_indices")
 
-    return (wf, outputs)
+    return wf, outputs
 
 
 def nuisance_regression(wf, cfg, strat_pool, pipe_num, opt, space, res=None):

CPAC/nuisance/utils/xfm.py

@@ -0,0 +1,69 @@
+# 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/>.
+"""Transformation utilities for nuisance regression."""
+
+from typing import cast, Literal
+
+from nipype.pipeline.engine import Workflow
+
+from CPAC.pipeline.engine import ResourcePool
+from CPAC.registration.registration import apply_transform
+from CPAC.utils.configuration import Configuration
+
+
+def transform_bold_mask_to_native(
+    wf: Workflow,
+    strat_pool: ResourcePool,
+    cfg: Configuration,
+    pipe_num: int,
+    reg_tool: Literal["ants", "fsl"],
+) -> tuple[Workflow, str]:
+    """Transform a template-space BOLD mask to native space."""
+    num_cpus = cast(
+        int, cfg["pipeline_setup", "system_config", "max_cores_per_participant"]
+    )
+    num_ants_cores = cast(
+        int, cfg["pipeline_setup", "system_config", "num_ants_threads"]
+    )
+    apply_xfm = apply_transform(
+        f"xfm_from-template_to-bold_mask_{pipe_num}",
+        reg_tool,
+        time_series=True,
+        num_cpus=num_cpus,
+        num_ants_cores=num_ants_cores,
+    )
+    apply_xfm.inputs.inputspec.interpolation = cfg[
+        "registration_workflows",
+        "functional_registration",
+        "func_registration_to_template",
+        f"{'ANTs' if reg_tool == 'ants' else 'FNIRT'}_pipelines",
+        "interpolation",
+    ]
+    sbref = strat_pool.node_data("sbref")
+    bold_mask = strat_pool.node_data(
+        ["space-template_desc-bold_mask", "space-template_desc-brain_mask"]
+    )
+    xfm = strat_pool.node_data("from-template_to-bold_mode-image_xfm")
+    wf.connect(
+        [
+            (bold_mask.node, apply_xfm, [(bold_mask.out, "inputspec.input_image")]),
+            (sbref.node, apply_xfm, [(sbref.out, "inputspec.reference")]),
+            (xfm.node, apply_xfm, [(xfm.out, "inputspec.transform")]),
+        ]
+    )
+
+    return apply_xfm, "outputspec.output_image"