From e78617b0d309198a9377fbb551cad447da39f35b Mon Sep 17 00:00:00 2001 From: mathiasg Date: Tue, 19 Apr 2022 14:29:57 -0400 Subject: [PATCH 1/2] CI: Use YAML anchors to avoid config duplication --- .circleci/config.yml | 446 +++++++++++++------------------------------ 1 file changed, 135 insertions(+), 311 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 0c75c23e7..a03dcbdd1 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -1,29 +1,102 @@ +# reusable anchors +_machine_defaults: &machine_defaults + environment: + TZ: "/usr/share/zoneinfo/America/Los_Angeles" + SCRATCH: "/scratch" + machine: + image: ubuntu-2004:current + docker_layer_caching: true + working_directory: /tmp/src/fmriprep + resource_class: large + +_python_defaults: &python_defaults + docker: + - image: circleci/python:3.9.6 + working_directory: /tmp/src/fmriprep + +_docker_auth: &docker_auth + name: Docker authentication + command: | + if [[ -n $DOCKER_PAT ]]; then + echo "$DOCKER_PAT" | docker login -u $DOCKER_USER --password-stdin + fi + +_setup_docker_registry: &setup_docker_registry + name: Set up Docker registry + command: | + if [[ -f /tmp/images/registry.tar.gz ]]; then + echo "Loading saved registry image" + docker load < /tmp/images/registry.tar.gz + else + echo "Pulling registry image from DockerHub" + docker pull registry:2 + fi + docker run -d -p 5000:5000 --restart=always --name=registry \ + -v /tmp/docker:/var/lib/registry registry:2 + +_pull_from_registry: &pull_from_registry + name: Pull and tag image from local registry + command: | + docker pull localhost:5000/fmriprep + docker tag localhost:5000/fmriprep nipreps/fmriprep:latest + +_check_skip_job: &check_skip_job + name: Check commit message and determine if job should be skipped + command: | + set -x +e + COMMIT_MSG="$(git log --format='format:%s' -n 1 $CIRCLE_SHA1)" + DOCBUILD="$(echo ${COMMIT_MSG} | grep -i -E '^docs?(\(\w+\))?:')" + SKIP_PYTEST="$(echo ${COMMIT_MSG} | grep -i -E '\[skip[ _]?tests\]')" + SKIP_DS005="$(echo ${COMMIT_MSG} | grep -i -E '\[skip[ _]?ds005\]' )" + SKIP_DS054="$(echo ${COMMIT_MSG} | grep -i -E '\[skip[ _]?ds054\]' )" + SKIP_DS210="$(echo ${COMMIT_MSG} | grep -i -E '\[skip[ _]?ds210\]' )" + NO_FASTTRACK="$(echo ${COMMIT_MSG} | grep -i -E '\[no[ _-]?fasttrack\]' )" + + # no skipping if tagged build + if [[ -n "$NO_FASTTRACK" ]]; then + touch /tmp/.nofasttrack + echo "Anatomical fasttrack reusing sMRIPrep's derivatives will not be used." + elif [[ -n "$CIRCLETAG" ]]; then + exit 0 + elif [[ -n "$DOCSBUILD" ]]; then # always try to skip docs builds + echo "Only docs build" + circleci step halt + elif [ -n "$CHECK_PYTEST" -a -n "$SKIP_PYTEST" ]; then + echo "Skipping pytest" + circleci step halt + elif [ -n "$CHECK_DS005" -a -n "$SKIP_DS005" ]; then + echo "Skipping DS005" + circleci step halt + elif [ -n "$CHECK_DS054" -a -n "$SKIP_DS054" ]; then + echo "Skipping DS054" + circleci step halt + elif [ -n "$CHECK_DS210" -a -n "$SKIP_DS210" ]; then + echo "Skipping DS210" + circleci step halt + fi + echo "No skip" + +_setup_fmriprep_docker: &setup_fmriprep_docker + name: Install fMRIPrep's docker wrapper + command: | + export PY3=$(pyenv versions | grep '3\.' | + sed -e 's/.* 3\./3./' -e 's/ .*//') + pyenv local $PY3 + mkdir -p /tmp/${DATASET}/derivatives + pip install --upgrade pip setuptools + pip install --upgrade /tmp/src/fmriprep/wrapper/ + + version: 2.1 orbs: docker: circleci/docker@1.6.0 jobs: build: - environment: - TZ: "/usr/share/zoneinfo/America/Los_Angeles" - SCRATCH: "/scratch" - machine: - # https://discuss.circleci.com/t/linux-machine-executor-images-2021-april-q2-update/39928 - # upgrade Docker version - image: ubuntu-2004:202104-01 - working_directory: /tmp/src/fmriprep + <<: *machine_defaults steps: - checkout - - run: - name: Check whether build should be skipped - command: | - set -x +e - COMMIT_MSG="$(git log --format='format:%s' -n 1 $CIRCLE_SHA1)" - DOCBUILD="$(echo ${COMMIT_MSG} | grep -i -E '^docs?(\(\w+\))?:')" - if [ -z "$CIRCLE_TAG" -a -n "$DOCBUILD" ]; then - echo "Only docs build" - circleci step halt - fi + - run: *check_skip_job - restore_cache: keys: - build-v5-{{ .Branch }}-{{ .Revision }} @@ -35,26 +108,15 @@ jobs: - /tmp/docker - /tmp/images - docker/install-docker-credential-helper + - run: *docker_auth + - run: *setup_docker_registry - run: - name: Docker authentication - command: | - if [[ -n $DOCKER_PAT ]]; then - echo "$DOCKER_PAT" | docker login -u $DOCKER_USER --password-stdin - fi - - run: - name: Set up Docker registry + name: Save docker registry command: | - if [[ -f /tmp/images/registry.tar.gz ]]; then - echo "Loading saved registry image" - docker load < /tmp/images/registry.tar.gz - else - echo "Pulling registry image from DockerHub" - docker pull registry:2 + if [[ ! -f /tmp/images/registry.tar.gz ]]; then mkdir -p /tmp/images docker save registry:2 | gzip > /tmp/images/registry.tar.gz fi - docker run -d -p 5000:5000 --restart=always --name=registry \ - -v /tmp/docker:/var/lib/registry registry:2 - run: name: Pull Ubuntu/focal image command: | @@ -135,9 +197,7 @@ jobs: - /tmp/images get_data: - machine: - image: ubuntu-2004:202104-01 - working_directory: /home/circleci/data + <<: *machine_defaults steps: - restore_cache: keys: @@ -253,29 +313,13 @@ jobs: - ds210/nipype.cfg test_pytest: - machine: - image: ubuntu-2004:202104-01 - working_directory: /tmp/src/fmriprep + <<: *machine_defaults + environment: + CHECK_PYTEST: true steps: - checkout: path: /home/circleci/src/fmriprep - - run: - name: Check whether build should be skipped - command: | - cd /home/circleci/src/fmriprep - set -x +e - COMMIT_MSG="$(git log --format='format:%s' -n 1 $CIRCLE_SHA1)" - DOCBUILD="$(echo ${COMMIT_MSG} | grep -i -E '^docs?(\(\w+\))?:')" - SKIP_PYTEST="$(echo ${COMMIT_MSG} | grep -i -E '\[skip[ _]?tests\]')" - if [ -z "$CIRCLE_TAG" -a -n "$DOCBUILD" ]; then - echo "Only docs build" - circleci step halt - fi - if [ -z "$CIRCLE_TAG" -a -n "$SKIP_PYTEST" ]; then - echo "Skipping pytest job" - circleci step halt - fi - + - run: *check_skip_job - attach_workspace: at: /tmp - restore_cache: @@ -288,29 +332,9 @@ jobs: keys: - data-v9-{{ .Branch }}-{{ .Revision }} - docker/install-docker-credential-helper - - run: - name: Docker authentication - command: | - if [[ -n $DOCKER_PAT ]]; then - echo "$DOCKER_PAT" | docker login -u $DOCKER_USER --password-stdin - fi - - run: - name: Set-up a Docker registry - command: | - if [[ -f /tmp/images/registry.tar.gz ]]; then - echo "Loading saved registry image" - docker load < /tmp/images/registry.tar.gz - else - echo "Pulling registry image from DockerHub" - docker pull registry:2 - fi - docker run -d -p 5000:5000 --restart=always --name=registry \ - -v /tmp/docker:/var/lib/registry registry:2 - - run: - name: Pull images from local registry - command: | - docker pull localhost:5000/fmriprep - docker tag localhost:5000/fmriprep nipreps/fmriprep:latest + - run: *docker_auth + - run: *setup_docker_registry + - run: *pull_from_registry - run: name: Run fMRIPrep tests no_output_timeout: 2h @@ -350,37 +374,16 @@ jobs: path: /tmp/data/reports ds005: - machine: - image: ubuntu-2004:202104-01 + <<: *machine_defaults working_directory: /tmp/ds005 environment: - FS_LICENSE: /tmp/fslicense/license.txt - DATASET: ds005 + - CHECK_DS005: true steps: - checkout: path: /home/circleci/src/fmriprep - - run: - name: Check whether build should be skipped or fast-tracked - command: | - cd /home/circleci/src/fmriprep - set -x +e - COMMIT_MSG="$(git log --format='format:%s' -n 1 $CIRCLE_SHA1)" - DOCBUILD="$(echo ${COMMIT_MSG} | grep -i -E '^docs?(\(\w+\))?:' )" - SKIP_DS005="$(echo ${COMMIT_MSG} | grep -i -E '\[skip[ _]?ds005\]' )" - NO_FASTTRACK="$(echo ${COMMIT_MSG} | grep -i -E '\[no[ _-]?fasttrack\]' )" - if [ -z "$CIRCLE_TAG" -a -n "$DOCBUILD" ]; then - echo "Only docs build" - circleci step halt - fi - if [ -z "$CIRCLE_TAG" -a -n "$SKIP_DS005" ]; then - echo "Skipping ds000005 build" - circleci step halt - fi - if [[ -n "$NO_FASTTRACK" ]]; then - touch /tmp/.nofasttrack - echo "Anatomical fasttrack reusing sMRIPrep's derivatives will not be used." - fi - + - run: *check_skip_job - attach_workspace: at: /tmp - restore_cache: @@ -400,38 +403,10 @@ jobs: - ds005-anat-v18-master- - ds005-anat-v18- - docker/install-docker-credential-helper - - run: - name: Docker authentication - command: | - if [[ -n $DOCKER_PAT ]]; then - echo "$DOCKER_PAT" | docker login -u $DOCKER_USER --password-stdin - fi - - run: - name: Set-up a Docker registry - command: | - if [[ -f /tmp/images/registry.tar.gz ]]; then - echo "Loading saved registry image" - docker load < /tmp/images/registry.tar.gz - else - echo "Pulling registry image from DockerHub" - docker pull registry:2 - fi - docker run -d -p 5000:5000 --restart=always --name=registry \ - -v /tmp/docker:/var/lib/registry registry:2 - - run: - name: Pull images from local registry - command: | - docker pull localhost:5000/fmriprep - docker tag localhost:5000/fmriprep nipreps/fmriprep:latest - - run: - name: Setting up test - command: | - export PY3=$(pyenv versions | grep '3\.' | - sed -e 's/.* 3\./3./' -e 's/ .*//') - pyenv local $PY3 - mkdir -p /tmp/${DATASET}/derivatives - pip install --upgrade pip setuptools - pip install --upgrade /tmp/src/fmriprep/wrapper/ + - run: *docker_auth + - run: *setup_docker_registry + - run: *pull_from_registry + - run: *setup_fmriprep_docker - run: name: Run anatomical workflow on ds005 no_output_timeout: 2h @@ -460,13 +435,11 @@ jobs: key: ds005-anat-v18-{{ .Branch }}-{{ .Revision }} paths: - /tmp/ds005/work - - run: name: Attempt run without PE metadata (should fail) no_output_timeout: 2h command: | echo "TODO" - - run: name: Run full fMRIPrep on ds005 (LegacyMultiProc plugin) no_output_timeout: 2h @@ -603,37 +576,20 @@ jobs: -exec sh -c 'rm -f {}; touch {}' \; find /tmp/${DATASET}/work_partial \( -name "*.nii.gz" -or -name "*.nii" -or -name "*.gii" -or -name "*.h5" \) \ -exec sh -c 'rm -f {}; touch {}' \; - - store_artifacts: path: /tmp/ds005/work ds054: - machine: - image: ubuntu-2004:202104-01 + <<: *machine_defaults working_directory: /tmp/ds054 environment: - FS_LICENSE: /tmp/fslicense/license.txt - DATASET: ds054 + - CHECK_DS054: true steps: - checkout: path: /home/circleci/src/fmriprep - - run: - name: Check whether build should be skipped - command: | - cd /home/circleci/src/fmriprep - set -x +e - COMMIT_MSG="$(git log --format='format:%s' -n 1 $CIRCLE_SHA1)" - DOCBUILD="$(echo ${COMMIT_MSG} | grep -i -E '^docs?(\(\w+\))?:')" - SKIP_DS054="$(echo ${COMMIT_MSG} | grep -i -E '\[skip[ _]?ds054\]' )" - if [ -z "$CIRCLE_TAG" -a -n "$DOCBUILD" ]; then - echo "Only docs build" - circleci step halt - fi - if [ -z "$CIRCLE_TAG" -a -n "$SKIP_DS054" ]; then - echo "Skipping ds000054 build" - circleci step halt - fi - + - run: *check_skip_job - attach_workspace: at: /tmp - restore_cache: @@ -652,39 +608,11 @@ jobs: - ds054-anat-v14-{{ .Branch }}- - ds054-anat-v14-master- - ds054-anat-v14- - - run: - name: Setting up test - command: | - export PY3=$(pyenv versions | grep '3\.' | - sed -e 's/.* 3\./3./' -e 's/ .*//') - pyenv local $PY3 - mkdir -p /tmp/${DATASET}/derivatives - pip install --upgrade pip setuptools - pip install --upgrade /tmp/src/fmriprep/wrapper/ - docker/install-docker-credential-helper - - run: - name: Docker authentication - command: | - if [[ -n $DOCKER_PAT ]]; then - echo "$DOCKER_PAT" | docker login -u $DOCKER_USER --password-stdin - fi - - run: - name: Set-up a Docker registry - command: | - if [[ -f /tmp/images/registry.tar.gz ]]; then - echo "Loading saved registry image" - docker load < /tmp/images/registry.tar.gz - else - echo "Pulling registry image from DockerHub" - docker pull registry:2 - fi - docker run -d -p 5000:5000 --restart=always --name=registry \ - -v /tmp/docker:/var/lib/registry registry:2 - - run: - name: Pull images from local registry - command: | - docker pull localhost:5000/fmriprep - docker tag localhost:5000/fmriprep nipreps/fmriprep:latest + - run: *docker_auth + - run: *setup_docker_registry + - run: *pull_from_registry + - run: *setup_fmriprep_docker - run: name: Run anatomical workflow on ds054 no_output_timeout: 2h @@ -777,32 +705,16 @@ jobs: path: /tmp/ds054 ds210: - machine: - image: ubuntu-2004:202104-01 + <<: *machine_defaults working_directory: /tmp/ds210 environment: - FS_LICENSE: /tmp/fslicense/license.txt - DATASET: ds210 + - CHECK_DS210: true steps: - checkout: path: /home/circleci/src/fmriprep - - run: - name: Check whether build should be skipped - command: | - cd /home/circleci/src/fmriprep - set -x +e - COMMIT_MSG="$(git log --format='format:%s' -n 1 $CIRCLE_SHA1)" - DOCBUILD="$(echo ${COMMIT_MSG} | grep -i -E '^docs?(\(\w+\))?:')" - SKIP_DS210="$(echo ${COMMIT_MSG} | grep -i -E '\[skip[ _]?ds054\]' )" - if [ -z "$CIRCLE_TAG" -a -n "$DOCBUILD" ]; then - echo "Only docs build" - circleci step halt - fi - if [ -z "$CIRCLE_TAG" -a -n "$SKIP_DS210" ]; then - echo "Skipping ds000210 build" - circleci step halt - fi - + - run: *check_skip_job - attach_workspace: at: /tmp - restore_cache: @@ -821,39 +733,11 @@ jobs: - ds210-anat-v12-{{ .Branch }}- - ds210-anat-v12-master- - ds210-anat-v12- - - run: - name: Setting up test - command: | - export PY3=$(pyenv versions | grep '3\.' | - sed -e 's/.* 3\./3./' -e 's/ .*//') - pyenv local $PY3 - mkdir -p /tmp/${DATASET}/derivatives - pip install --upgrade pip setuptools - pip install --upgrade /tmp/src/fmriprep/wrapper/ - docker/install-docker-credential-helper - - run: - name: Docker authentication - command: | - if [[ -n $DOCKER_PAT ]]; then - echo "$DOCKER_PAT" | docker login -u $DOCKER_USER --password-stdin - fi - - run: - name: Set-up a Docker registry - command: | - if [[ -f /tmp/images/registry.tar.gz ]]; then - echo "Loading saved registry image" - docker load < /tmp/images/registry.tar.gz - else - echo "Pulling registry image from DockerHub" - docker pull registry:2 - fi - docker run -d -p 5000:5000 --restart=always --name=registry \ - -v /tmp/docker:/var/lib/registry registry:2 - - run: - name: Pull images from local registry - command: | - docker pull localhost:5000/fmriprep - docker tag localhost:5000/fmriprep nipreps/fmriprep:latest + - run: *docker_auth + - run: *setup_docker_registry + - run: *pull_from_registry + - run: *setup_fmriprep_docker - run: name: Run anatomical workflow on ds000210 no_output_timeout: 2h @@ -939,11 +823,9 @@ jobs: path: /tmp/ds210 deploy_docker_patches: - machine: - image: ubuntu-2004:202104-01 + <<: *machine_defaults working_directory: /tmp/src/fmriprep steps: - - run: name: Check whether image should be deployed to Docker Hub command: | @@ -951,8 +833,6 @@ jobs: echo "Nothing to deploy for $CIRCLE_PROJECT_USERNAME/$CIRCLE_PROJECT_REPONAME." circleci step halt fi - - checkout: - path: /home/circleci/src/fmriprep - restore_cache: keys: - build-v5-{{ .Branch }}-{{ .Revision }} @@ -960,29 +840,9 @@ jobs: - /tmp/docker - /tmp/images - docker/install-docker-credential-helper - - run: - name: Docker authentication - command: | - if [[ -n $DOCKER_PAT ]]; then - echo "$DOCKER_PAT" | docker login -u $DOCKER_USER --password-stdin - fi - - run: - name: Setup a Docker registry - command: | - if [[ -f /tmp/images/registry.tar.gz ]]; then - echo "Loading saved registry image" - docker load < /tmp/images/registry.tar.gz - else - echo "Pulling registry image from DockerHub" - docker pull registry:2 - fi - docker run -d -p 5000:5000 --restart=always --name=registry \ - -v /tmp/docker:/var/lib/registry registry:2 - - run: - name: Pull images from local registry - command: | - docker pull localhost:5000/fmriprep - docker tag localhost:5000/fmriprep nipreps/fmriprep:latest + - run: *docker_auth + - run: *setup_docker_registry + - run: *pull_from_registry - run: name: Deploy to Docker Hub no_output_timeout: 40m @@ -991,23 +851,11 @@ jobs: docker push nipreps/fmriprep:${CIRCLE_BRANCH#docker/} deploy_docker: - machine: - image: ubuntu-2004:202104-01 - working_directory: /tmp/src/fmriprep + <<: *machine_defaults steps: - checkout: path: /home/circleci/src/fmriprep - - run: - name: Check whether build should be skipped - command: | - cd /home/circleci/src/fmriprep - set -x +e - COMMIT_MSG="$(git log --format='format:%s' -n 1 $CIRCLE_SHA1)" - DOCBUILD="$(echo ${COMMIT_MSG} | grep -i -E '^docs?(\(\w+\))?:')" - if [ -z "$CIRCLE_TAG" -a -n "$DOCBUILD" ]; then - echo "Only docs build" - circleci step halt - fi + - run: *check_skip_job - restore_cache: keys: - build-v5-{{ .Branch }}-{{ .Revision }} @@ -1015,29 +863,9 @@ jobs: - /tmp/docker - /tmp/images - docker/install-docker-credential-helper - - run: - name: Docker authentication - command: | - if [[ -n $DOCKER_PAT ]]; then - echo "$DOCKER_PAT" | docker login -u $DOCKER_USER --password-stdin - fi - - run: - name: Set-up a Docker registry - command: | - if [[ -f /tmp/images/registry.tar.gz ]]; then - echo "Loading saved registry image" - docker load < /tmp/images/registry.tar.gz - else - echo "Pulling registry image from DockerHub" - docker pull registry:2 - fi - docker run -d -p 5000:5000 --restart=always --name=registry \ - -v /tmp/docker:/var/lib/registry registry:2 - - run: - name: Pull images from local registry - command: | - docker pull localhost:5000/fmriprep - docker tag localhost:5000/fmriprep nipreps/fmriprep:latest + - run: *docker_auth + - run: *setup_docker_registry + - run: *pull_from_registry - run: name: Deploy to Docker Hub no_output_timeout: 40m @@ -1054,9 +882,7 @@ jobs: fi test_deploy_pypi: - docker: - - image: cimg/python:3.9 - working_directory: /tmp/src/fmriprep + <<: *python_defaults steps: - checkout - run: @@ -1113,9 +939,7 @@ jobs: path: /tmp/src/fmriprep/wrapper/dist deploy_pypi: - docker: - - image: cimg/python:3.9 - working_directory: /tmp/src/fmriprep + <<: *python_defaults steps: - checkout - run: From 5c087bb9c3adb6dc773e65a55b4c0d6d60682051 Mon Sep 17 00:00:00 2001 From: mathiasg Date: Tue, 19 Apr 2022 14:41:38 -0400 Subject: [PATCH 2/2] CI: Increase resources available to fMRIPrep runs --- .circleci/config.yml | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index a03dcbdd1..1798aba79 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -422,8 +422,8 @@ jobs: --fs-subjects-dir /tmp/${DATASET}/freesurfer \ --skull-strip-template OASIS30ANTs:res-1 \ --output-spaces MNI152NLin2009cAsym MNI152NLin6Asym \ - --sloppy --write-graph --mem_mb 4096 \ - --nthreads 2 --anat-only -vv + --sloppy --write-graph --mem-mb 14336 \ + --nthreads 4 --anat-only -vv fi - run: name: Clean-up after anatomical run @@ -462,11 +462,11 @@ jobs: --fs-subjects-dir /tmp/${DATASET}/freesurfer \ ${FASTRACK_ARG} \ --output-layout legacy \ - --sloppy --write-graph --mem_mb 4096 \ + --sloppy --write-graph --mem-mb 14336 \ --skull-strip-template OASIS30ANTs:res-1 \ --output-spaces fsaverage5 fsnative \ --use-plugin /home/circleci/src/fmriprep/.circleci/legacy.yml \ - --nthreads 2 -vv + --nthreads 4 -vv - store_artifacts: path: /tmp/ds005/derivatives destination: full-run @@ -507,9 +507,9 @@ jobs: --config $PWD/nipype.cfg -w /tmp/${DATASET}/work_bids \ /tmp/data/${DATASET}/ /tmp/${DATASET}/bids participant \ ${FASTRACK_ARG} \ - --sloppy --write-graph --mem_mb 4096 \ + --sloppy --write-graph --mem-mb 14336 \ --output-spaces fsaverage5 \ - --nthreads 2 -vv + --nthreads 4 -vv - store_artifacts: path: /tmp/ds005/bids destination: bids-run @@ -541,10 +541,10 @@ jobs: --fs-subjects-dir /tmp/${DATASET}/freesurfer \ ${FASTRACK_ARG} \ --output-layout legacy \ - --sloppy --write-graph --use-syn-sdc --mem_mb 4096 \ + --sloppy --write-graph --use-syn-sdc --mem-mb 14336 \ --output-spaces MNI152NLin2009cAsym fsaverage5 fsnative MNI152NLin6Asym anat \ --aroma-melodic-dimensionality 2 --use-aroma \ - --nthreads 2 --cifti-output -vv + --nthreads 4 --cifti-output -vv - store_artifacts: path: /tmp/ds005/derivatives_partial destination: partial-run @@ -626,7 +626,7 @@ jobs: --output-layout legacy \ --fs-no-reconall --sloppy --write-graph \ --output-spaces MNI152NLin2009cAsym \ - --mem_mb 4096 --nthreads 2 --anat-only -vv + --mem-mb 14336 --nthreads 4 --anat-only -vv fi - run: name: Clean-up after anatomical run @@ -655,7 +655,7 @@ jobs: --output-layout legacy \ --fs-no-reconall --sloppy \ --output-spaces MNI152NLin2009cAsym:res-2 anat func \ - --mem_mb 4096 --nthreads 2 -vv --debug compcor + --mem-mb 14336 --nthreads 4 -vv --debug compcor - run: name: Checking outputs of fMRIPrep command: | @@ -751,7 +751,7 @@ jobs: --output-layout legacy \ --fs-no-reconall --sloppy --write-graph \ --output-spaces MNI152NLin2009cAsym \ - --mem_mb 4096 --nthreads 2 --anat-only -vv + --mem-mb 14336 --nthreads 4 --anat-only -vv fi - run: name: Clean-up after anatomical run @@ -794,7 +794,7 @@ jobs: --fs-no-reconall --use-syn-sdc --ignore slicetiming \ --dummy-scans 1 --sloppy --write-graph \ --output-spaces MNI152NLin2009cAsym \ - --mem_mb 4096 --nthreads 2 -vv + --mem-mb 14336 --nthreads 4 -vv - run: name: Checking outputs of fMRIPrep command: |