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Merge remote-tracking branch 'upstream/master' into enh/3dvolreg
2 parents 145bde0 + 8f73452 commit e9de427

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‎.circleci/config.yml

Lines changed: 73 additions & 29 deletions
Original file line numberDiff line numberDiff line change
@@ -354,10 +354,10 @@ jobs:
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at: /tmp
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- restore_cache:
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keys:
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- ds005-anat-v8-{{ .Branch }}-{{ epoch }}
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- ds005-anat-v8-{{ .Branch }}
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- ds005-anat-v8-master
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- ds005-anat-v8-
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- ds005-anat-v9-{{ .Branch }}-{{ epoch }}
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- ds005-anat-v9-{{ .Branch }}
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- ds005-anat-v9-master
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- ds005-anat-v9-
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- run:
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name: Setting up test
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command: |
@@ -388,10 +388,10 @@ jobs:
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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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/tmp/data/ds005 /tmp/ds005/derivatives participant \
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--debug --write-graph --mem_mb 4096 \
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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-v8-{{ .Branch }}-{{ epoch }}
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key: ds005-anat-v9-{{ .Branch }}-{{ epoch }}
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paths:
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- /tmp/ds005/work
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- /tmp/ds005/derivatives/fmriprep
@@ -408,7 +408,7 @@ jobs:
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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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/tmp/data/ds005 /tmp/ds005/derivatives participant \
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--debug --write-graph --use-syn-sdc --mem_mb 4096 \
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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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--output-space T1w template fsaverage5 \
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--template-resampling-grid native \
@@ -435,7 +435,7 @@ jobs:
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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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/tmp/data/ds005 /tmp/ds005/derivatives_partial participant \
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--debug --write-graph --use-syn-sdc --mem_mb 4096 \
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--sloppy --write-graph --use-syn-sdc --mem_mb 4096 \
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--output-space T1w template fsaverage5 \
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--ignore-aroma-denoising-errors --use-aroma \
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--template-resampling-grid native \
@@ -483,10 +483,10 @@ jobs:
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at: /tmp
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- restore_cache:
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keys:
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- ds054-anat-v6-{{ .Branch }}-{{ epoch }}
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- ds054-anat-v6-{{ .Branch }}
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- ds054-anat-v6-master
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- ds054-anat-v6-
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- ds054-anat-v7-{{ .Branch }}-{{ epoch }}
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- ds054-anat-v7-{{ .Branch }}
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- ds054-anat-v7-master
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- ds054-anat-v7-
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- run:
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name: Setting up test
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command: |
@@ -517,10 +517,10 @@ jobs:
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-e FMRIPREP_DEV 1 \
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--config $PWD/nipype.cfg -w /tmp/ds054/work \
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/tmp/data/ds054 /tmp/ds054/derivatives participant \
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--fs-no-reconall --debug --write-graph \
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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-v6-{{ .Branch }}-{{ epoch }}
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key: ds054-anat-v7-{{ .Branch }}-{{ epoch }}
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paths:
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- /tmp/ds054/work
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- /tmp/ds054/derivatives
@@ -537,7 +537,7 @@ jobs:
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-e FMRIPREP_DEV 1 \
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--config $PWD/nipype.cfg -w /tmp/ds054/work \
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/tmp/data/ds054 /tmp/ds054/derivatives participant \
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--fs-no-reconall --debug \
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--fs-no-reconall --sloppy \
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--output-space T1w template \
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--template-resampling-grid 2mm \
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--mem_mb 4096 --nthreads 2 -vv
@@ -562,7 +562,7 @@ jobs:
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-e FMRIPREP_DEV 1 \
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--config $PWD/nipype.cfg -w /tmp/ds054/work \
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/tmp/data/ds054 /tmp/ds054/derivatives participant \
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--fs-no-reconall --debug --write-graph \
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--fs-no-reconall --sloppy --write-graph \
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--output-space T1w template \
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--template-resampling-grid 2mm \
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--reports-only --run-uuid $UUID
@@ -601,8 +601,8 @@ jobs:
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at: /tmp
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- restore_cache:
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keys:
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- ds210-anat-v3-{{ epoch }}
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- ds210-anat-v3-
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- ds210-anat-v4-{{ epoch }}
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- ds210-anat-v4-
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- run:
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name: Setting up test
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command: |
@@ -633,10 +633,10 @@ jobs:
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-e FMRIPREP_DEV 1 \
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--config $PWD/nipype.cfg -w /tmp/ds210/work \
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/tmp/data/ds210 /tmp/ds210/derivatives participant \
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--fs-no-reconall --debug --write-graph \
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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-v3-{{ epoch }}
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key: ds210-anat-v4-{{ epoch }}
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paths:
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- /tmp/ds210/work
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- /tmp/ds210/derivatives
@@ -651,7 +651,7 @@ jobs:
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/tmp/data/ds210 /tmp/ds210/derivatives participant \
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--fs-no-reconall --t2s-coreg --use-syn-sdc \
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--template-resampling-grid native \
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--debug --write-graph --mem_mb 4096 --nthreads 2 -vv
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--sloppy --write-graph --mem_mb 4096 --nthreads 2 -vv
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- run:
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name: Checking outputs of fMRIPrep
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command: |
@@ -670,7 +670,7 @@ jobs:
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- store_artifacts:
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path: /tmp/ds210
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deploy:
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deploy_docker:
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machine:
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image: circleci/classic:201711-01
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working_directory: /tmp/src/fmriprep
@@ -694,10 +694,22 @@ jobs:
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command: |
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if [[ -n "$DOCKER_PASS" ]]; then
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docker login -u $DOCKER_USER -p $DOCKER_PASS
697-
docker push poldracklab/fmriprep:latest
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docker tag poldracklab/fmriprep poldracklab/fmriprep:$CIRCLE_TAG
699-
docker push poldracklab/fmriprep:$CIRCLE_TAG
697+
docker tag poldracklab/fmriprep poldracklab/fmriprep:unstable
698+
docker push poldracklab/fmriprep:unstable
699+
if [[ -n "$CIRCLE_TAG" ]]; then
700+
docker push poldracklab/fmriprep:latest
701+
docker tag poldracklab/fmriprep poldracklab/fmriprep:$CIRCLE_TAG
702+
docker push poldracklab/fmriprep:$CIRCLE_TAG
703+
fi
700704
fi
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deploy_pypi:
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machine:
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image: circleci/classic:201711-01
709+
working_directory: /tmp/src/fmriprep
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steps:
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- attach_workspace:
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at: /tmp
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- run:
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name: Deploy to PyPi
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command: |
@@ -730,14 +742,22 @@ workflows:
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- get_regression_data:
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filters:
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branches:
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ignore: /docs?\/.*/
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ignore:
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- /docs?\/.*/
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- /ds005\/.*/
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- /ds054\/.*/
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- /ds210\/.*/
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- build_docs:
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requires:
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- build
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filters:
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branches:
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ignore: /tests?\/.*/
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ignore:
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- /tests?\/.*/
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- /ds005\/.*/
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- /ds054\/.*/
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- /ds210\/.*/
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tags:
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only: /.*/
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@@ -758,7 +778,11 @@ workflows:
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- get_regression_data
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filters:
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branches:
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ignore: /docs?\/.*/
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ignore:
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- /docs?\/.*/
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- /ds005\/.*/
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- /ds054\/.*/
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- /ds210\/.*/
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tags:
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only: /.*/
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@@ -771,6 +795,8 @@ workflows:
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ignore:
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- /docs?\/.*/
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- /tests?\/.*/
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- /ds054\/.*/
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- /ds210\/.*/
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tags:
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only: /.*/
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@@ -783,6 +809,8 @@ workflows:
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ignore:
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- /docs?\/.*/
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- /tests?\/.*/
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- /ds005\/.*/
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- /ds210\/.*/
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tags:
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only: /.*/
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@@ -796,10 +824,26 @@ workflows:
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ignore:
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- /docs?\/.*/
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- /tests?\/.*/
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- /ds005\/.*/
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- /ds054\/.*/
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tags:
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only: /.*/
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- deploy_docker:
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requires:
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- build
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- test_pytest
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- build_docs
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- ds005
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- ds054
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- ds210
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filters:
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branches:
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only: master
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tags:
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only: /.*/
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802-
- deploy:
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- deploy_pypi:
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requires:
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- build
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- test_pytest

‎.circleci/ds005_outputs.txt

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@@ -6,64 +6,64 @@ fmriprep/logs/CITATION.md
66
fmriprep/logs/CITATION.tex
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fmriprep/sub-01
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fmriprep/sub-01/anat
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fmriprep/sub-01/anat/sub-01_brainmask.nii.gz
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fmriprep/sub-01/anat/sub-01_class-CSF_probtissue.nii.gz
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fmriprep/sub-01/anat/sub-01_class-GM_probtissue.nii.gz
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fmriprep/sub-01/anat/sub-01_class-WM_probtissue.nii.gz
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fmriprep/sub-01/anat/sub-01_dtissue.nii.gz
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fmriprep/sub-01/anat/sub-01_inflated.L.surf.gii
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fmriprep/sub-01/anat/sub-01_inflated.R.surf.gii
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fmriprep/sub-01/anat/sub-01_label-aparcaseg_roi.nii.gz
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fmriprep/sub-01/anat/sub-01_label-aseg_roi.nii.gz
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fmriprep/sub-01/anat/sub-01_midthickness.L.surf.gii
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fmriprep/sub-01/anat/sub-01_midthickness.R.surf.gii
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fmriprep/sub-01/anat/sub-01_pial.L.surf.gii
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fmriprep/sub-01/anat/sub-01_pial.R.surf.gii
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fmriprep/sub-01/anat/sub-01_preproc.nii.gz
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fmriprep/sub-01/anat/sub-01_smoothwm.L.surf.gii
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fmriprep/sub-01/anat/sub-01_smoothwm.R.surf.gii
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fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_brainmask.nii.gz
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fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_class-CSF_probtissue.nii.gz
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fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_class-GM_probtissue.nii.gz
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fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_class-WM_probtissue.nii.gz
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fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_dtissue.nii.gz
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fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_preproc.nii.gz
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fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_target-T1w_warp.h5
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fmriprep/sub-01/anat/sub-01_space-orig_target-T1w_affine.txt
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fmriprep/sub-01/anat/sub-01_target-fsnative_affine.txt
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fmriprep/sub-01/anat/sub-01_target-MNI152NLin2009cAsym_warp.h5
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fmriprep/sub-01/anat/sub-01_desc-brain_mask.nii.gz
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fmriprep/sub-01/anat/sub-01_desc-preproc_T1w.nii.gz
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fmriprep/sub-01/anat/sub-01_dseg.nii.gz
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fmriprep/sub-01/anat/sub-01_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5
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fmriprep/sub-01/anat/sub-01_from-orig_to-T1w_mode-image_xfm.txt
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fmriprep/sub-01/anat/sub-01_from-T1w_to-fsnative_mode-image_xfm.txt
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fmriprep/sub-01/anat/sub-01_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5
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fmriprep/sub-01/anat/sub-01_hemi-L_inflated.surf.gii
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fmriprep/sub-01/anat/sub-01_hemi-L_midthickness.surf.gii
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fmriprep/sub-01/anat/sub-01_hemi-L_pial.surf.gii
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fmriprep/sub-01/anat/sub-01_hemi-L_smoothwm.surf.gii
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fmriprep/sub-01/anat/sub-01_hemi-R_inflated.surf.gii
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fmriprep/sub-01/anat/sub-01_hemi-R_midthickness.surf.gii
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fmriprep/sub-01/anat/sub-01_hemi-R_pial.surf.gii
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fmriprep/sub-01/anat/sub-01_hemi-R_smoothwm.surf.gii
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fmriprep/sub-01/anat/sub-01_label-aparcaseg_dseg.nii.gz
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fmriprep/sub-01/anat/sub-01_label-aseg_dseg.nii.gz
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fmriprep/sub-01/anat/sub-01_label-CSF_probseg.nii.gz
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fmriprep/sub-01/anat/sub-01_label-GM_probseg.nii.gz
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fmriprep/sub-01/anat/sub-01_label-WM_probseg.nii.gz
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fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
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fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz
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fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_dseg.nii.gz
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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_confounds.tsv
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_MELODICmix.tsv
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-cifti_variant-space1_preproc.dtseries.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-cifti_variant-space1_preproc.dtseries.nii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-fsaverage5.L.func.gii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-fsaverage5.R.func.gii
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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-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_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-MNI152NLin2009cAsym_boldref.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_brainmask.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_preproc.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_variant-smoothAROMAnonaggr_preproc.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_brainmask.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_label-aparcaseg_roi.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_label-aseg_roi.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_preproc.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-01_space-T1w_label-aparcaseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_label-aseg_dseg.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_confounds.tsv
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_MELODICmix.tsv
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-cifti_variant-space1_preproc.dtseries.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-cifti_variant-space1_preproc.dtseries.nii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsaverage5.L.func.gii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsaverage5.R.func.gii
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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
55+
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_regressors.tsv
56+
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-MELODIC_mixing.tsv
57+
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-MNI152NLin2009cAsym_boldref.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_brainmask.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_preproc.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_variant-smoothAROMAnonaggr_preproc.nii.gz
60+
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_label-aseg_dseg.nii.gz
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fmriprep/sub-01.html
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/tmp/ds005/derivatives

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