Merge branch 'develop' into feature/total_readout_time

Author: sgiavasis

.github/Dockerfiles/C-PAC.develop-ABCD-HCP-bionic.Dockerfile

@@ -1,9 +1,8 @@
-FROM ghcr.io/fcp-indi/c-pac/stage-base:abcd-hcp-v1.8.4
+FROM ghcr.io/fcp-indi/c-pac/stage-base:abcd-hcp-v1.8.5.dev
 LABEL org.opencontainers.image.description "Full C-PAC image with software dependencies version-matched to [ABCD-HCP BIDS fMRI Pipeline](https://github.com/DCAN-Labs/abcd-hcp-pipeline/blob/e480a8f99534f1b05f37bf44c64827384b69b383/Dockerfile)"
 USER root
 
 # install C-PAC
-COPY dev/docker_data/default_pipeline.yml /cpac_resources/default_pipeline.yml
 COPY dev/circleci_data/pipe-test_ci.yml /cpac_resources/pipe-test_ci.yml
 COPY . /code
 RUN pip install -e /code

.github/Dockerfiles/C-PAC.develop-bionic.Dockerfile

@@ -1,9 +1,8 @@
-FROM ghcr.io/fcp-indi/c-pac/stage-base:standard-v1.8.4
+FROM ghcr.io/fcp-indi/c-pac/stage-base:standard-v1.8.5.dev
 LABEL org.opencontainers.image.description "Full C-PAC image"
 USER root
 
 # install C-PAC
-COPY dev/docker_data/default_pipeline.yml /cpac_resources/default_pipeline.yml
 COPY dev/circleci_data/pipe-test_ci.yml /cpac_resources/pipe-test_ci.yml
 COPY . /code
 RUN pip install -e /code

.github/Dockerfiles/C-PAC.develop-fMRIPrep-LTS-xenial.Dockerfile

@@ -1,9 +1,8 @@
-FROM ghcr.io/fcp-indi/c-pac/stage-base:fmriprep-lts-v1.8.4
+FROM ghcr.io/fcp-indi/c-pac/stage-base:fmriprep-lts-v1.8.5.dev
 LABEL org.opencontainers.image.description "Full C-PAC image with software dependencies version-matched to [fMRIPrep LTS](https://reproducibility.stanford.edu/fmriprep-lts#long-term-support-lts)"
 USER root
 
 # install C-PAC & set up runscript
-COPY dev/docker_data/default_pipeline.yml /cpac_resources/default_pipeline.yml
 COPY dev/circleci_data/pipe-test_ci.yml /cpac_resources/pipe-test_ci.yml
 COPY . /code
 RUN pip install -e /code

.github/Dockerfiles/Ubuntu.bionic-non-free.Dockerfile

@@ -1,5 +1,7 @@
+FROM ghcr.io/fcp-indi/c-pac_templates:latest as c-pac_templates
 FROM neurodebian:bionic-non-free AS dcan-hcp
 
+
 ARG DEBIAN_FRONTEND=noninteractive
 
 # Adding DCAN dependencies & HCP code
@@ -145,10 +147,15 @@ RUN conda update conda -y && \
     git lfs install
 
 # Installing C-PAC templates and atlases
-COPY --from=ghcr.io/fcp-indi/c-pac_templates:latest /cpac_templates /cpac_templates
+COPY --from=c-pac_templates /cpac_templates /cpac_templates
 COPY --from=dcan-hcp /opt/dcan-tools/pipeline/global /opt/dcan-tools/pipeline/global
 COPY --from=ghcr.io/fcp-indi/c-pac/neuroparc:v1.0-human /ndmg_atlases /ndmg_atlases
 
+# Installing surface files for downsampling
+COPY --from=c-pac_templates /opt/dcan-tools/pipeline/global/templates/standard_mesh_atlases/ /opt/dcan-tools/pipeline/global/templates/standard_mesh_atlases/
+COPY --from=c-pac_templates /opt/dcan-tools/pipeline/global/templates/Greyordinates/ /opt/dcan-tools/pipeline/global/templates/Greyordinates/
+
+
 ENTRYPOINT ["/bin/bash"]
 
 # Link libraries for Singularity images

.github/Dockerfiles/Ubuntu.xenial-20200114.Dockerfile

@@ -1,3 +1,4 @@
+FROM ghcr.io/fcp-indi/c-pac_templates:latest as c-pac_templates
 FROM nipreps/fmriprep:20.2.1 as fmriprep
 FROM ubuntu:xenial-20200114 AS dcan-hcp
 
@@ -156,9 +157,13 @@ RUN pip install -r /opt/requirements.txt
 RUN pip install xvfbwrapper
 
 # install cpac templates
-COPY --from=ghcr.io/fcp-indi/c-pac_templates:latest /cpac_templates /cpac_templates
+COPY --from=c-pac_templates /cpac_templates /cpac_templates
 COPY --from=dcan-hcp /opt/dcan-tools/pipeline/global /opt/dcan-tools/pipeline/global
 
+# Installing surface files for downsampling
+COPY --from=c-pac_templates /opt/dcan-tools/pipeline/global/templates/standard_mesh_atlases/ /opt/dcan-tools/pipeline/global/templates/standard_mesh_atlases/
+COPY --from=c-pac_templates /opt/dcan-tools/pipeline/global/templates/Greyordinates/ /opt/dcan-tools/pipeline/global/templates/Greyordinates/
+
 RUN curl -s https://packagecloud.io/install/repositories/github/git-lfs/script.deb.sh | bash
 RUN apt-get install git-lfs
 RUN git lfs install

.github/workflows/check_updated_version.yml

@@ -44,9 +44,8 @@ jobs:
             VERSION=$(python -c "from info import __version__; print('.'.join(('.'.join(__version__[::-1].split('-')[1].split('.')[1:])[::-1], __version__.split('-')[1])) if '-' in __version__ else __version__)")
             cd ..
             echo "v${VERSION}" > version
-            sed -i -r "s/^(# [Vv]ersion ).*$/# Version ${VERSION}/g" dev/docker_data/default_pipeline.yml
             find ./CPAC/resources/configs -name "*.yml" -exec sed -i -r "s/^(# [Vv]ersion ).*$/# Version ${VERSION}/g" {} \;
-            git add version CPAC/resources/configs dev/docker_data/default_pipeline.yml
+            git add version CPAC/resources/configs
             if [[ ! -z $(git diff origin/${GITHUB_BRANCH}) ]]
             then
               git commit -m ":bookmark: Update version to ${VERSION} ($COMMIT_MESSAGE)"

.gitignore

@@ -17,9 +17,6 @@ develop-eggs
 .installed.cfg
 .env*
 
-# Copy from packaging
-CPAC/resources/configs/default_pipeline.yml
-
 # Installer logs
 pip-log.txt
 

.pylintrc

@@ -428,18 +428,25 @@ function-naming-style=snake_case
 # Good variable names which should always be accepted, separated by a comma.
 good-names=c,
            e,
+           f,
            i,
            j,
            k,
            ex,
            nb,
            Run,
+           TR,
+           v,
            wf,
            _,
 
 # Good variable names regexes, separated by a comma. If names match any regex,
 # they will always be accepted
-good-names-rgxs=^_version_(extra|m[a-n]{2}[or]{2})$  # version parts in info.py
+good-names-rgxs=^_version_(extra|m[a-n]{2}[or]{2})$,  # version parts in info.py
+                .*EPI.*,
+                .*TE.*,
+                .*T1.*,
+                .*T2.*
 
 # Include a hint for the correct naming format with invalid-name.
 include-naming-hint=yes

CHANGELOG.md

@@ -14,13 +14,29 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## unreleased
+## [unreleased]
 
 ### Added
+- Added the ability to downsample to 10K or 2K resolution for freesurfer runs
 - Added the ability to ingress TotalReadoutTime from epi field map meta-data from the JSON sidecars.
 - Added the ability to use TotalReadoutTime of epi field maps in the calculation of FSL topup distortion correction.
+- Difference method (``-``) for ``CPAC.utils.configuration.Configuration`` instances
+
+### Changed
+- Added a level of depth to `working` directories to match `log` and `output` directory structure
+- Renamed participant-pipeline-level `output` directory prefix to `pipeline_` to match `log` and `working` paths
+- Changed the 1mm atlases chosen in the rbc-options preconfig to the 2mm versions
+- For Nilearn-generated correlation matrices, diagonals are now set to all `1`s (were all `0`s)
+- Added ability to apply nusiance correction to template-space BOLD images
+- Removed ability to run single-step-resampling on motion-corrected BOLD data
+- Moved default pipeline config into directory with other preconfigs
+- Added crash messages from during and before graph building to logs
+- Added data-config-specific hash string to C-PAC-generated config files
+- Updated `rbc-options` preconfig to use `fmriprep-options` preprocessing
 
 ### Fixed
+- Fixed [bug](https://github.com/FCP-INDI/C-PAC/issues/1795) that was causing `cpac run` to fail when passing a manual random seed via `--random_seed`.
+- Replaces ``DwellTime`` with ``EffectiveEchoSpacing`` for FSL usage of the term
 - Fixed an issue that was causing some epi field maps to not be ingressed if the BIDS tags were not in the correct order.
 
 ## [v1.8.4] - 2022-06-27

CPAC/alff/alff.py

@@ -246,8 +246,8 @@ def alff_falff(wf, cfg, strat_pool, pipe_num, opt=None):
      "switch": ["run"],
      "option_key": "None",
      "option_val": "None",
-     "inputs": [["desc-cleaned_bold", "desc-brain_bold", "desc-preproc_bold",
-                 "bold"],
+     "inputs": [["desc-cleanedNofilt_bold", "desc-brain_bold", 
+                 "desc-preproc_bold", "bold"],
                 "space-bold_desc-brain_mask"],
      "outputs": ["alff",
                  "falff"]}
@@ -262,7 +262,7 @@ def alff_falff(wf, cfg, strat_pool, pipe_num, opt=None):
     alff.get_node('hp_input').iterables = ('hp', alff.inputs.hp_input.hp)
     alff.get_node('lp_input').iterables = ('lp', alff.inputs.lp_input.lp)
 
-    node, out = strat_pool.get_data(["desc-cleaned_bold", "desc-brain_bold",
+    node, out = strat_pool.get_data(["desc-cleanedNofilt_bold", "desc-brain_bold",
                                      "desc-preproc_bold", "bold"])
     wf.connect(node, out, alff, 'inputspec.rest_res')