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DOCKER: Include 3T18yoSchwartzReactN32 FreeSurfer atlas in image #357

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merged 2 commits into from
Aug 16, 2023
Merged

DOCKER: Include 3T18yoSchwartzReactN32 FreeSurfer atlas in image #357

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7a43bc2
DOCKER: Include 3T18yoSchwartzReactN32 FreeSurfer atlas in image
psadil Aug 16, 2023
22a230f
pin circleci machine image, matching fmriprep
psadil Aug 16, 2023
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19 changes: 9 additions & 10 deletions .circleci/config.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ _machine_defaults: &machine_defaults
TZ: "/usr/share/zoneinfo/America/Los_Angeles"
SCRATCH: "/scratch"
machine:
image: ubuntu-2204:current
image: ubuntu-2204:2023.04.2
docker_layer_caching: true
working_directory: /tmp/src/smriprep
resource_class: large
Expand Down Expand Up @@ -159,8 +159,8 @@ jobs:
paths:
- src/smriprep
- save_cache:
key: build-v1-{{ .Branch }}-{{ .Revision }}
paths:
key: build-v1-{{ .Branch }}-{{ .Revision }}
paths:
- /tmp/docker
- /tmp/images

Expand All @@ -176,8 +176,8 @@ jobs:
docker exec -it registry /bin/registry garbage-collect --delete-untagged \
/etc/docker/registry/config.yml
- save_cache:
key: build-v1-{{ .Branch }}-{{ .Revision }}
paths:
key: build-v1-{{ .Branch }}-{{ .Revision }}
paths:
- /tmp/docker
- /tmp/images

Expand Down Expand Up @@ -468,8 +468,8 @@ jobs:
rm -rf /tmp/ds005/work/reportlets
rm -rf /tmp/ds005/work/smriprep_wf/fsdir_run_*/
- save_cache:
key: ds005-anat-v9-{{ .Branch }}-{{ epoch }}
paths:
key: ds005-anat-v9-{{ .Branch }}-{{ epoch }}
paths:
- /tmp/ds005/work

- run:
Expand Down Expand Up @@ -600,8 +600,8 @@ jobs:
sudo chown $(id -un):$(id -gn) -R /tmp/ds054
rm -rf /tmp/ds054/work/reportlets
- save_cache:
key: ds054-anat-v7-{{ .Branch }}-{{ epoch }}
paths:
key: ds054-anat-v7-{{ .Branch }}-{{ epoch }}
paths:
- /tmp/ds054/work
- run:
name: Checking outputs of sMRIPrep
Expand Down Expand Up @@ -845,7 +845,6 @@ workflows:
tags:
only: /.*/


- deploy_docs_master:
requires:
- build_docs
Expand Down
6 changes: 0 additions & 6 deletions docker/files/freesurfer7.3.2-exclude.txt
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Original file line number Diff line number Diff line change
@@ -1,9 +1,3 @@
freesurfer/average/3T18yoSchwartzReactN32_as_orig.4dfp.hdr
freesurfer/average/3T18yoSchwartzReactN32_as_orig.4dfp.ifh
freesurfer/average/3T18yoSchwartzReactN32_as_orig.4dfp.img
freesurfer/average/3T18yoSchwartzReactN32_as_orig.4dfp.img.rec
freesurfer/average/3T18yoSchwartzReactN32_as_orig.4dfp.mat
freesurfer/average/3T18yoSchwartzReactN32_as_orig.lst
freesurfer/average/711-2B_as_mni_average_305.4dfp.hdr
freesurfer/average/711-2B_as_mni_average_305.4dfp.ifh
freesurfer/average/711-2B_as_mni_average_305.4dfp.img
Expand Down
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