Merge pull request #2230 from FCP-INDI/organism

👔🔧 Add "organism" to pipeline config

Author: sgiavasis

.circleci/main.yml

@@ -119,7 +119,7 @@ commands:
           coverage-file: .coverage.docker${VARIANT}
       - run:
           name: Running pytest in Docker image
-          command: docker exec --user $(id -u) docker_test /bin/bash /code/dev/circleci_data/test_in_image.sh
+          command: docker exec -e OSF_DATA --user $(id -u) docker_test /bin/bash /code/dev/circleci_data/test_in_image.sh
   set-python-version:
     steps:
       - restore_cache:

.github/Dockerfiles/base-lite.Dockerfile

@@ -1,4 +1,4 @@
-# Copyright (C) 2023  C-PAC Developers
+# Copyright (C) 2023-2025  C-PAC Developers
 
 # This file is part of C-PAC.
 
@@ -14,12 +14,12 @@
 
 # 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/>.
-FROM ghcr.io/fcp-indi/c-pac/afni:23.3.09-jammy as AFNI
-FROM ghcr.io/fcp-indi/c-pac/ants:2.4.3-jammy as ANTs
-FROM ghcr.io/fcp-indi/c-pac/c3d:1.0.0-jammy as c3d
-FROM ghcr.io/fcp-indi/c-pac/connectome-workbench:1.5.0.neurodebian-jammy as connectome-workbench
-FROM ghcr.io/fcp-indi/c-pac/fsl:6.0.6.5-jammy as FSL
-FROM ghcr.io/fcp-indi/c-pac/ica-aroma:0.4.4-beta-jammy as ICA-AROMA
+FROM ghcr.io/fcp-indi/c-pac/afni:23.3.09-jammy AS afni
+FROM ghcr.io/fcp-indi/c-pac/ants:2.4.3-jammy AS ants
+FROM ghcr.io/fcp-indi/c-pac/c3d:1.0.0-jammy AS c3d
+FROM ghcr.io/fcp-indi/c-pac/connectome-workbench:1.5.0.neurodebian-jammy AS connectome-workbench
+FROM ghcr.io/fcp-indi/c-pac/fsl:6.0.6.5-jammy AS fsl
+FROM ghcr.io/fcp-indi/c-pac/ica-aroma:0.4.4-beta-jammy AS ica-aroma
 
 FROM ghcr.io/fcp-indi/c-pac/ubuntu:jammy-non-free
 LABEL org.opencontainers.image.description="NOT INTENDED FOR USE OTHER THAN AS A STAGE IMAGE IN A MULTI-STAGE BUILD \
@@ -47,11 +47,11 @@ ENV FSLTCLSH=$FSLDIR/bin/fsltclsh \
     PATH=${FSLDIR}/bin:$PATH \
     TZ=America/New_York \
     USER=c-pac_user
-COPY --from=FSL /lib/x86_64-linux-gnu /lib/x86_64-linux-gnu
-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
+COPY --from=fsl /lib/x86_64-linux-gnu /lib/x86_64-linux-gnu
+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
 
 # Installing C-PAC dependencies
 COPY requirements.txt /opt/requirements.txt
@@ -67,10 +67,10 @@ ENV C3DPATH /opt/c3d
 ENV PATH $C3DPATH/bin:$PATH
 
 # Installing AFNI
-COPY --from=AFNI /lib/x86_64-linux-gnu/ld* /lib/x86_64-linux-gnu/
-COPY --from=AFNI /lib/x86_64-linux-gnu/lib*so* /lib/x86_64-linux-gnu/
-COPY --from=AFNI /lib64/ld* /lib64/
-COPY --from=AFNI /opt/afni/ /opt/afni/
+COPY --from=afni /lib/x86_64-linux-gnu/ld* /lib/x86_64-linux-gnu/
+COPY --from=afni /lib/x86_64-linux-gnu/lib*so* /lib/x86_64-linux-gnu/
+COPY --from=afni /lib64/ld* /lib64/
+COPY --from=afni /opt/afni/ /opt/afni/
 # set up AFNI
 ENV PATH=/opt/afni:$PATH
 
@@ -79,11 +79,11 @@ ENV LANG="en_US.UTF-8" \
     LC_ALL="en_US.UTF-8" \
     ANTSPATH=/usr/lib/ants/bin \
     PATH=/usr/lib/ants/bin:$PATH
-COPY --from=ANTs /usr/lib/ants/ /usr/lib/ants/
-COPY --from=ANTs /ants_template/ /ants_template/
+COPY --from=ants /usr/lib/ants/ /usr/lib/ants/
+COPY --from=ants /ants_template/ /ants_template/
 
 # Installing ICA-AROMA
-COPY --from=ICA-AROMA /opt/ICA-AROMA/ /opt/ICA-AROMA/
+COPY --from=ica-aroma /opt/ICA-AROMA/ /opt/ICA-AROMA/
 ENV PATH=/opt/ICA-AROMA:$PATH
 
 # link libraries & clean up

.github/Dockerfiles/base-standard.Dockerfile

@@ -46,9 +46,9 @@ COPY dev/docker_data/license.txt $FREESURFER_HOME/license.txt
 RUN apt-get autoremove -y \
     && apt-get autoclean -y \
     && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* /root/.cache/* \
+    && ln -s /usr/lib/x86_64-linux-gnu/libcrypt.so.1 /usr/lib/x86_64-linux-gnu/libcrypt.so.2 \
     && find / -type f -print0 | sort -t/ -k2 | xargs -0 rdfind -makehardlinks true \
     && rm -rf results.txt \
-    && cp -l /lib/x86_64-linux-gnu/libcrypt.so.1.1.0 /lib/x86_64-linux-gnu/libcrypt.so.2 \
     && ldconfig \
     && chmod 777 / /home/c-pac_user \
     && chmod 777 $(ls / | grep -v sys | grep -v proc)

.github/dependabot.yaml

@@ -1,3 +1,19 @@
+# Copyright (C) 2024 - 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/>.
 version: 2
 registries:
   ghcr:

CHANGELOG.md

@@ -31,6 +31,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - `censor_file_path` from `offending_timepoints_connector` in the `build_nuisance_regressor` node.
 - 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.
 
 ### Changed
 
@@ -69,6 +70,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - 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.
 
+### Upgraded dependencies
+
+- `voluptuous` 0.13.1 → 0.15.2
+
 ### Removed
 
 - Variant image recipes.
@@ -83,6 +88,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Inputs `[desc-motion_bold, bold]` from `coregistration_prep_vol` nodeblock.
 - `input` field from `coregistration` in blank and default config.
 - `reg_with_skull` swtich from `func_input_prep` in blank and default config.
+- Support for AFNI 3dECM < v21.1.1.
+- `calculate_motion_before` and `calculate_motion_after` configuration options.
 
 #### Removed CI dependency
 

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/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.
 
@@ -25,7 +25,6 @@
 from CPAC.pipeline.nodeblock import nodeblock
 from CPAC.registration.registration 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"]
 

CPAC/func_preproc/__init__.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.
 
@@ -19,20 +19,20 @@
 from .func_motion import (
     calc_motion_stats,
     func_motion_correct,
-    func_motion_correct_only,
     func_motion_estimates,
-    get_motion_ref,
+    get_motion_refs,
     motion_estimate_filter,
+    stack_motion_blocks,
 )
 from .func_preproc import get_idx, slice_timing_wf
 
 __all__ = [
     "calc_motion_stats",
     "func_motion_correct",
-    "func_motion_correct_only",
     "func_motion_estimates",
     "get_idx",
-    "get_motion_ref",
+    "get_motion_refs",
     "motion_estimate_filter",
     "slice_timing_wf",
+    "stack_motion_blocks",
 ]