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[skip ci] update documentation to reflect new confounds options
2 parents d9c33e9 + 38d0550 commit 69a7908

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‎.circleci/config.yml

Lines changed: 70 additions & 25 deletions
Original file line numberDiff line numberDiff line change
@@ -257,8 +257,8 @@ jobs:
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-e FMRIPREP_REGRESSION_TARGETS=/tmp/data/fmriprep_bold_mask \
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-e FMRIPREP_REGRESSION_REPORTS=/tmp/data/reports \
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--entrypoint="py.test" poldracklab/fmriprep:latest \
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/root/src/fmriprep/ \
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-svx --doctest-modules --ignore=/root/src/fmriprep/docs --ignore=setup.py
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/src/fmriprep/ \
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-svx --doctest-modules --ignore=/src/fmriprep/docs --ignore=setup.py
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- run:
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name: Package new masks
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no_output_timeout: 10m
@@ -329,7 +329,7 @@ jobs:
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docker run -ti --rm=false -v $PWD:/_build_html \
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--entrypoint=sphinx-build poldracklab/fmriprep:latest \
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-T -E -b html -d _build/doctrees-readthedocs -W -D \
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language=en /root/src/fmriprep/docs/ /_build_html 2>&1 \
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language=en /src/fmriprep/docs/ /_build_html 2>&1 \
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| tee $PWD/builddocs.log
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cat $PWD/builddocs.log
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grep -qv "ERROR" $PWD/builddocs.log
@@ -358,10 +358,10 @@ jobs:
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at: /tmp
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- restore_cache:
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keys:
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- ds005-anat-v13-{{ .Branch }}-{{ epoch }}
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- ds005-anat-v13-{{ .Branch }}
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- ds005-anat-v13-master
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- ds005-anat-v13-
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- ds005-anat-v14-{{ .Branch }}-{{ epoch }}
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- ds005-anat-v14-{{ .Branch }}
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- ds005-anat-v14-master
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- ds005-anat-v14-
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- run:
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name: Setting up test
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command: |
@@ -389,13 +389,13 @@ jobs:
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sudo setfacl -d -m group:$(id -gn):rwx /tmp/ds005/work && \
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sudo setfacl -m group:$(id -gn):rwx /tmp/ds005/work
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fmriprep-docker -i poldracklab/fmriprep:latest \
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-e FMRIPREP_DEV 1 -u $(id -u) \
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-e FMRIPREP_DEV 1 \
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--config $PWD/nipype.cfg -w /tmp/ds005/work \
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/tmp/data/ds005 /tmp/ds005/derivatives participant \
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--sloppy --write-graph --mem_mb 4096 \
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--nthreads 2 --anat-only -vv
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- save_cache:
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key: ds005-anat-v13-{{ .Branch }}-{{ epoch }}
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key: ds005-anat-v14-{{ .Branch }}-{{ epoch }}
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paths:
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- /tmp/ds005/work
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@@ -408,11 +408,11 @@ jobs:
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sudo setfacl -d -m group:$(id -gn):rwx /tmp/ds005/work && \
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sudo setfacl -m group:$(id -gn):rwx /tmp/ds005/work
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fmriprep-docker -i poldracklab/fmriprep:latest \
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-e FMRIPREP_DEV 1 -u $(id -u) \
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-e FMRIPREP_DEV 1 \
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--config $PWD/nipype.cfg -w /tmp/ds005/work \
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/tmp/data/ds005 /tmp/ds005/derivatives participant \
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--sloppy --write-graph --use-syn-sdc --mem_mb 4096 \
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--ignore-aroma-denoising-errors --use-aroma \
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--use-aroma \
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--output-space T1w template fsaverage5 fsnative \
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--template-resampling-grid native \
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--use-plugin /home/circleci/src/fmriprep/.circleci/legacy.yml \
@@ -423,6 +423,7 @@ jobs:
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mkdir -p /tmp/ds005/derivatives_partial
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sudo mv /tmp/ds005/derivatives/freesurfer /tmp/ds005/derivatives_partial
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sudo cp -a /tmp/ds005/work /tmp/ds005/work_partial
426+
sudo rm -rf /tmp/ds005/work_partial/fmriprep_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_wf/ica_aroma_wf
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- run:
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name: Checking outputs of full fMRIPrep run
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command: |
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name: Re-run fMRIPrep on single run of task data
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no_output_timeout: 2h
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command: |
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rm /tmp/data/ds005/sub-01/func/*_run-02_*
438+
rm /tmp/data/ds005/sub-01/func/*_run-01_*
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fmriprep-docker -i poldracklab/fmriprep:latest \
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-e FMRIPREP_DEV 1 -u $(id -u) \
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--config $PWD/nipype.cfg -w /tmp/ds005/work \
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-e FMRIPREP_DEV 1 \
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--config $PWD/nipype.cfg -w /tmp/ds005/work_partial \
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/tmp/data/ds005 /tmp/ds005/derivatives_partial participant \
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--sloppy --write-graph --use-syn-sdc --mem_mb 4096 \
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--output-space T1w template fsaverage5 fsnative \
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--ignore-aroma-denoising-errors --use-aroma \
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--aroma-melodic-dimensionality 2 --use-aroma \
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--template-resampling-grid native \
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--nthreads 2 --cifti-output -vv
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- run:
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at: /tmp
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- restore_cache:
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keys:
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- ds054-anat-v11-{{ .Branch }}-{{ epoch }}
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- ds054-anat-v11-{{ .Branch }}
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- ds054-anat-v11-master
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- ds054-anat-v11-
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- ds054-anat-v12-{{ .Branch }}-{{ epoch }}
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- ds054-anat-v12-{{ .Branch }}
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- ds054-anat-v12-master
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- ds054-anat-v12-
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- run:
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name: Setting up test
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command: |
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--fs-no-reconall --sloppy --write-graph \
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--mem_mb 4096 --nthreads 2 --anat-only -vv
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- save_cache:
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key: ds054-anat-v11-{{ .Branch }}-{{ epoch }}
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key: ds054-anat-v12-{{ .Branch }}-{{ epoch }}
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paths:
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- /tmp/ds054/work
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at: /tmp
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- restore_cache:
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keys:
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- ds210-anat-v9-{{ .Branch }}-{{ epoch }}
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- ds210-anat-v9-{{ .Branch }}
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- ds210-anat-v9-master
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- ds210-anat-v9-
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- ds210-anat-v10-{{ .Branch }}-{{ epoch }}
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- ds210-anat-v10-{{ .Branch }}
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- ds210-anat-v10-master
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- ds210-anat-v10-
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- run:
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name: Setting up test
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command: |
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--fs-no-reconall --sloppy --write-graph \
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--mem_mb 4096 --nthreads 2 --anat-only -vv
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- save_cache:
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key: ds210-anat-v9-{{ .Branch }}-{{ epoch }}
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key: ds210-anat-v10-{{ .Branch }}-{{ epoch }}
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paths:
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- /tmp/ds210/work
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@@ -676,6 +677,35 @@ jobs:
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- store_artifacts:
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path: /tmp/ds210
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680+
deploy_docker_patches:
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machine:
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image: circleci/classic:201711-01
683+
working_directory: /tmp/src/fmriprep
684+
steps:
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686+
- attach_workspace:
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at: /tmp
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- run:
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name: Load Docker image layer cache
690+
no_output_timeout: 30m
691+
command: |
692+
docker info
693+
set +o pipefail
694+
if [ -f /tmp/cache/docker.tar.gz ]; then
695+
sudo apt update && sudo apt -y install pigz
696+
pigz -d --stdout /tmp/cache/docker.tar.gz | docker load
697+
docker images
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fi
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- run:
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name: Deploy to Docker Hub
701+
no_output_timeout: 40m
702+
command: |
703+
if [[ -n "$DOCKER_PASS" ]]; then
704+
docker login -u $DOCKER_USER -p $DOCKER_PASS
705+
docker tag poldracklab/fmriprep poldracklab/fmriprep:${CIRCLE_BRANCH#docker/}
706+
docker push poldracklab/fmriprep:${CIRCLE_BRANCH#docker/}
707+
fi
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deploy_docker:
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machine:
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image: circleci/classic:201711-01
@@ -746,6 +776,7 @@ workflows:
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ignore:
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- /docs?\/.*/
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- /tests?\/.*/
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- /docker\/.*/
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tags:
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only: /.*/
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@@ -757,6 +788,7 @@ workflows:
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- /ds005\/.*/
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- /ds054\/.*/
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- /ds210\/.*/
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- /docker\/.*/
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tags:
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only: /.*/
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@@ -770,6 +802,7 @@ workflows:
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- /ds005\/.*/
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- /ds054\/.*/
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- /ds210\/.*/
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- /docker\/.*/
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tags:
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only: /.*/
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ignore:
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- /docs?\/.*/
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- /tests?\/.*/
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- /docker\/.*/
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tags:
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only: /.*/
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@@ -795,6 +829,7 @@ workflows:
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- /ds005\/.*/
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- /ds054\/.*/
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- /ds210\/.*/
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- /docker\/.*/
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tags:
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only: /.*/
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@@ -809,6 +844,7 @@ workflows:
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- /tests?\/.*/
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- /ds054\/.*/
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- /ds210\/.*/
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- /docker\/.*/
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tags:
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only: /.*/
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- /tests?\/.*/
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- /ds005\/.*/
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- /ds210\/.*/
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- /docker\/.*/
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tags:
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only: /.*/
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@@ -838,9 +875,17 @@ workflows:
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- /tests?\/.*/
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- /ds005\/.*/
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- /ds054\/.*/
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- /docker\/.*/
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tags:
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only: /.*/
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- deploy_docker_patches:
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requires:
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- build
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filters:
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branches:
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only: /docker\/.*/
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- deploy_docker:
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requires:
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- build

‎.circleci/ds005_partial_outputs.txt

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@@ -34,27 +34,25 @@ fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz
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fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz
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fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz
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fmriprep/sub-01/func
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_AROMAnoiseICs.csv
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold.dtseries.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold.dtseries.nii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-acompcor_decomposition.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_regressors.tsv
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-MELODIC_mixing.tsv
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-tcompcor_decomposition.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-fsaverage5_hemi-L.func.gii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-fsaverage5_hemi-R.func.gii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-fsnative_hemi-L.func.gii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-fsnative_hemi-R.func.gii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_boldref.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_desc-aparcaseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_desc-aseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_boldref.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_desc-aparcaseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_desc-aseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_desc-brain_mask.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_desc-preproc_bold.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_AROMAnoiseICs.csv
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold.dtseries.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold.dtseries.nii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_regressors.tsv
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-MELODIC_mixing.tsv
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsaverage5_hemi-L.func.gii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsaverage5_hemi-R.func.gii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsnative_hemi-L.func.gii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsnative_hemi-R.func.gii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_boldref.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-aparcaseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-aseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_boldref.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-aparcaseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-aseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-brain_mask.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-preproc_bold.nii.gz
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fmriprep/sub-01.html
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/tmp/ds005/derivatives_partial

‎CHANGES.rst

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@@ -1,3 +1,27 @@
1+
1.3.0.post1 (February 8, 2019)
2+
==============================
3+
4+
Hotfix release intended for Singularity users. For further detail, please see
5+
`#1500 <https://github.com/poldracklab/fmriprep/issues/1500>`__.
6+
7+
1.3.0 (February 7, 2019)
8+
========================
9+
10+
We start the 1.3.x series including a few bugfixes, housekeeping duty and a refactors
11+
to leverage `sMRIPrep <https://github.com/poldracklab/smriprep>`__ (which is a fork of
12+
fMRIPrep's anatomical workflow), pybids>=0.7 for querying dataset, and
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`TemplateFlow <https://github.com/templateflow>`__ for handling standard spaces.
14+
15+
* [FIX] Bad ``fsnative`` replacement in CIfTI workflow (#1476) @oesteban
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* [FIX] Avoid warning when generating boilerplate (#1464) @oesteban
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* [MAINT] resolves #1485 : patch fmriprep-docker automount for use with Python 3.7 (#1486) @rciric
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* [RF] Use anatomical workflows from sMRIPrep (#1482) @oesteban
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* [MAINT] Update sentry-sdk (#1490) @chrisfilo
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* [ENH] Remaining TemplateFlow integrations (#1494) @oesteban
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* [MAINT] Update to keep up with poldracklab/niworkflows#299 (#1496) @oesteban
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* [FIX] Updating bids-validator to 1.1.3 (#1498) @chrisfilo
23+
24+
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1.2.6-1 (January 24, 2019)
226
==========================
327

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