Merge branch 'develop' into fix/check_s3

Author: birajstha

.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

.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

@@ -32,6 +32,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Switch `sink_native_transforms` under `registration_workflows` to output all `.mat` files in ANTs and FSL Transforms.
 - `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
 
@@ -55,6 +58,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   - 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`.
   - Upgraded resource retrieval to `importlib.resources`.
+- 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
 
@@ -70,6 +76,8 @@ 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.
+- `Freesufer-ABCD` brain masking strategy to create mask as per the original DCAN script.
+- A bug where `$ANTSPATH` was unset in C-PAC with FreeSurfer images.
 
 ### Upgraded dependencies
 

CPAC/anat_preproc/anat_preproc.py

@@ -1128,37 +1128,12 @@ def freesurfer_abcd_brain_connector(wf, cfg, strat_pool, pipe_num, opt):
         name=f"wmparc_to_nifti_{pipe_num}",
     )
 
-    # Register wmparc file if ingressing FreeSurfer data
-    if strat_pool.check_rpool("pipeline-fs_xfm"):
-        wmparc_to_native = pe.Node(
-            Function(
-                input_names=["source_file", "target_file", "xfm", "out_file"],
-                output_names=["transformed_file"],
-                function=normalize_wmparc,
-            ),
-            name=f"wmparc_to_native_{pipe_num}",
-        )
-
-        wmparc_to_native.inputs.out_file = "wmparc_warped.mgz"
-
-        node, out = strat_pool.get_data("pipeline-fs_wmparc")
-        wf.connect(node, out, wmparc_to_native, "source_file")
-
-        node, out = strat_pool.get_data("pipeline-fs_raw-average")
-        wf.connect(node, out, wmparc_to_native, "target_file")
-
-        node, out = strat_pool.get_data("pipeline-fs_xfm")
-        wf.connect(node, out, wmparc_to_native, "xfm")
-
-        wf.connect(wmparc_to_native, "transformed_file", wmparc_to_nifti, "in_file")
-
-    else:
-        node, out = strat_pool.get_data("pipeline-fs_wmparc")
-        wf.connect(node, out, wmparc_to_nifti, "in_file")
+    node, out = strat_pool.get_data("pipeline-fs_wmparc")
+    wf.connect(node, out, wmparc_to_nifti, "in_file")
 
     wmparc_to_nifti.inputs.args = "-rt nearest"
 
-    node, out = strat_pool.get_data("desc-preproc_T1w")
+    node, out = strat_pool.get_data(["desc-restore_T1w", "desc-preproc_T1w"])
     wf.connect(node, out, wmparc_to_nifti, "reslice_like")
 
     binary_mask = pe.Node(
@@ -1194,7 +1169,7 @@ def freesurfer_abcd_brain_connector(wf, cfg, strat_pool, pipe_num, opt):
 
     wf.connect(binary_filled_mask, "out_file", brain_mask_to_t1_restore, "in_file")
 
-    node, out = strat_pool.get_data("desc-preproc_T1w")
+    node, out = strat_pool.get_data(["desc-restore_T1w", "desc-preproc_T1w"])
     wf.connect(node, out, brain_mask_to_t1_restore, "ref_file")
 
     outputs = {"space-T1w_desc-brain_mask": (brain_mask_to_t1_restore, "out_file")}
@@ -1303,7 +1278,7 @@ def freesurfer_fsl_brain_connector(wf, cfg, strat_pool, pipe_num, opt):
     # fslmaths tmp_mask.nii.gz -mas ${CCSDIR}/templates/MNI152_T1_1mm_first_brain_mask.nii.gz tmp_mask.nii.gz
     apply_mask = pe.Node(interface=fsl.maths.ApplyMask(), name=f"apply_mask_{node_id}")
 
-    wf.connect(skullstrip, "out_file", apply_mask, "in_file")
+    wf.connect(skullstrip, "mask_file", apply_mask, "in_file")
 
     node, out = strat_pool.get_data("T1w-brain-template-mask-ccs")
     wf.connect(node, out, apply_mask, "mask_file")
@@ -1347,36 +1322,18 @@ def freesurfer_fsl_brain_connector(wf, cfg, strat_pool, pipe_num, opt):
 
     wf.connect(combine_mask, "out_file", binarize_combined_mask, "in_file")
 
-    # CCS brain mask is in FS space, transfer it back to native T1 space
-    fs_fsl_brain_mask_to_native = pe.Node(
-        interface=freesurfer.ApplyVolTransform(),
-        name=f"fs_fsl_brain_mask_to_native_{node_id}",
-    )
-    fs_fsl_brain_mask_to_native.inputs.reg_header = True
-    fs_fsl_brain_mask_to_native.inputs.interp = "nearest"
-
-    wf.connect(
-        binarize_combined_mask, "out_file", fs_fsl_brain_mask_to_native, "source_file"
-    )
-
-    node, out = strat_pool.get_data("pipeline-fs_raw-average")
-    wf.connect(node, out, fs_fsl_brain_mask_to_native, "target_file")
-
-    node, out = strat_pool.get_data("freesurfer-subject-dir")
-    wf.connect(node, out, fs_fsl_brain_mask_to_native, "subjects_dir")
-
     if opt == "FreeSurfer-BET-Tight":
         outputs = {
             "space-T1w_desc-tight_brain_mask": (
-                fs_fsl_brain_mask_to_native,
-                "transformed_file",
+                binarize_combined_mask,
+                "out_file",
             )
         }
     elif opt == "FreeSurfer-BET-Loose":
         outputs = {
             "space-T1w_desc-loose_brain_mask": (
-                fs_fsl_brain_mask_to_native,
-                "transformed_file",
+                binarize_combined_mask,
+                "out_file",
             )
         }
 
@@ -2028,10 +1985,9 @@ def brain_mask_acpc_freesurfer(wf, cfg, strat_pool, pipe_num, opt=None):
     option_key=["anatomical_preproc", "brain_extraction", "using"],
     option_val="FreeSurfer-ABCD",
     inputs=[
-        "desc-preproc_T1w",
+        ["desc-restore_T1w", "desc-preproc_T1w"],
         "pipeline-fs_wmparc",
         "pipeline-fs_raw-average",
-        "pipeline-fs_xfm",
         "freesurfer-subject-dir",
     ],
     outputs=["space-T1w_desc-brain_mask"],
@@ -2058,11 +2014,21 @@ def brain_mask_freesurfer_abcd(wf, cfg, strat_pool, pipe_num, opt=None):
         "T1w-brain-template-mask-ccs",
         "T1w-ACPC-template",
     ],
-    outputs=["space-T1w_desc-tight_brain_mask"],
+    outputs={
+        "space-T1w_desc-brain_mask": {
+            "Description": "Brain mask extracted using FreeSurfer-BET-Tight method",
+            "Method": "FreeSurfer-BET-Tight",
+            "Threshold": "tight",
+        }
+    },
 )
 def brain_mask_freesurfer_fsl_tight(wf, cfg, strat_pool, pipe_num, opt=None):
     wf, outputs = freesurfer_fsl_brain_connector(wf, cfg, strat_pool, pipe_num, opt)
 
+    # Convert the tight brain mask to generic brain mask
+    outputs["space-T1w_desc-brain_mask"] = outputs.pop(
+        "space-T1w_desc-tight_brain_mask"
+    )
     return (wf, outputs)
 
 
@@ -2075,10 +2041,9 @@ def brain_mask_freesurfer_fsl_tight(wf, cfg, strat_pool, pipe_num, opt=None):
     option_key=["anatomical_preproc", "brain_extraction", "using"],
     option_val="FreeSurfer-ABCD",
     inputs=[
-        "desc-preproc_T1w",
+        ["desc-restore_T1w", "desc-preproc_T1w"],
         "pipeline-fs_wmparc",
         "pipeline-fs_raw-average",
-        "pipeline-fs_xfm",
         "freesurfer-subject-dir",
     ],
     outputs=["space-T1w_desc-acpcbrain_mask"],
@@ -2107,11 +2072,21 @@ def brain_mask_acpc_freesurfer_abcd(wf, cfg, strat_pool, pipe_num, opt=None):
         "T1w-brain-template-mask-ccs",
         "T1w-ACPC-template",
     ],
-    outputs=["space-T1w_desc-loose_brain_mask"],
+    outputs={
+        "space-T1w_desc-brain_mask": {
+            "Description": "Brain mask extracted using FreeSurfer-BET-Loose method",
+            "Method": "FreeSurfer-BET-Loose",
+            "Threshold": "loose",
+        }
+    },
 )
 def brain_mask_freesurfer_fsl_loose(wf, cfg, strat_pool, pipe_num, opt=None):
     wf, outputs = freesurfer_fsl_brain_connector(wf, cfg, strat_pool, pipe_num, opt)
 
+    # Convert the loose brain mask to generic brain mask
+    outputs["space-T1w_desc-brain_mask"] = outputs.pop(
+        "space-T1w_desc-loose_brain_mask"
+    )
     return (wf, outputs)
 
 
@@ -2187,7 +2162,6 @@ 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):
@@ -2225,7 +2199,6 @@ 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/anat_preproc/tests/test_anat_preproc.py

@@ -5,6 +5,11 @@
 import nibabel as nib
 
 from .. import anat_preproc
+from unittest.mock import Mock, patch
+from ..anat_preproc import (
+    brain_mask_freesurfer_fsl_loose,
+    brain_mask_freesurfer_fsl_tight,
+)
 
 
 class TestAnatPreproc:
@@ -269,3 +274,71 @@ def test_anat_brain(self):
             # print 'correlation: ', correlation
 
             assert correlation[0, 1] >= 0.97
+
+
+@patch("CPAC.anat_preproc.anat_preproc.freesurfer_fsl_brain_connector")
+def test_brain_mask_freesurfer_fsl_loose(mock_connector):
+    """Test that brain_mask_freesurfer_fsl_loose correctly renames output key."""
+
+    mock_wf = Mock()
+    mock_cfg = Mock()
+    mock_strat_pool = Mock()
+    pipe_num = 1
+
+    mock_outputs = {
+        "space-T1w_desc-loose_brain_mask": "brain_mask_data",
+        "other_output": "other_data",
+    }
+
+    mock_connector.return_value = (mock_wf, mock_outputs)
+
+    result_wf, result_outputs = brain_mask_freesurfer_fsl_loose(
+        mock_wf, mock_cfg, mock_strat_pool, pipe_num
+    )
+
+    mock_connector.assert_called_once_with(
+        mock_wf, mock_cfg, mock_strat_pool, pipe_num, None
+    )
+
+    # Assert workflow returned unchanged
+    assert result_wf == mock_wf
+
+    # Assert output key was renamed correctly
+    assert "space-T1w_desc-brain_mask" in result_outputs
+    assert "space-T1w_desc-loose_brain_mask" not in result_outputs
+    assert result_outputs["space-T1w_desc-brain_mask"] == "brain_mask_data"
+    assert result_outputs["other_output"] == "other_data"
+
+
+@patch("CPAC.anat_preproc.anat_preproc.freesurfer_fsl_brain_connector")
+def test_brain_mask_freesurfer_fsl_tight(mock_connector):
+    """Test that brain_mask_freesurfer_fsl_tight correctly renames output key."""
+
+    mock_wf = Mock()
+    mock_cfg = Mock()
+    mock_strat_pool = Mock()
+    pipe_num = 1
+
+    mock_outputs = {
+        "space-T1w_desc-tight_brain_mask": "brain_mask_data",
+        "other_output": "other_data",
+    }
+
+    mock_connector.return_value = (mock_wf, mock_outputs)
+
+    result_wf, result_outputs = brain_mask_freesurfer_fsl_tight(
+        mock_wf, mock_cfg, mock_strat_pool, pipe_num
+    )
+
+    mock_connector.assert_called_once_with(
+        mock_wf, mock_cfg, mock_strat_pool, pipe_num, None
+    )
+
+    # Assert workflow returned unchanged
+    assert result_wf == mock_wf
+
+    # Assert output key was renamed correctly
+    assert "space-T1w_desc-brain_mask" in result_outputs
+    assert "space-T1w_desc-tight_brain_mask" not in result_outputs
+    assert result_outputs["space-T1w_desc-brain_mask"] == "brain_mask_data"
+    assert result_outputs["other_output"] == "other_data"

CPAC/anat_preproc/utils.py

@@ -487,7 +487,9 @@ def mri_convert(in_file, reslice_like=None, out_file=None, args=None):
     import os
 
     if out_file is None:
-        out_file = in_file.replace(".mgz", ".nii.gz")
+        out_file = os.path.join(
+            os.getcwd(), os.path.basename(in_file).replace(".mgz", ".nii.gz")
+        )
 
     cmd = "mri_convert %s %s" % (in_file, out_file)
 
@@ -525,7 +527,9 @@ def mri_convert_reorient(in_file, orientation, out_file=None):
     import os
 
     if out_file is None:
-        out_file = in_file.split(".")[0] + "_reoriented.mgz"
+        out_file = os.path.join(
+            os.getcwd(), os.path.basename(in_file).split(".")[0] + "_reoriented.mgz"
+        )
 
     cmd = "mri_convert %s %s --out_orientation %s" % (in_file, out_file, orientation)