Started Running as brainvisa ---------------------------------------- $ /usr/bin/python3 /volatile/a-sac-ns-brainvisa/bbi_nightly/cea-master-5.3/src/development/casa-distro/master/bin/casa_distro bv_maker name=cea-master-5.3 -- sources ---------------------------------------- Updating git repository /casa/host/src/aims/aims-free/master $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Already up to date. Updating git repository /casa/host/src/aims/aims-gpl/master $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Already up to date. Updating git repository /casa/host/src/anatomist/anatomist-free/master $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Already up to date. Updating git repository /casa/host/src/anatomist/anatomist-gpl/master $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Already up to date. Updating git repository /casa/host/src/axon/master $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Already up to date. Updating git repository /casa/host/src/brainrat/bioprocessing/master $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' Using BioProj credentials stored in svn.secret (username 'brainvisa-admin') $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Already up to date. Updating git repository /casa/host/src/brainrat/brainrat-gpl/master $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' Using BioProj credentials stored in svn.secret (username 'brainvisa-admin') $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Already up to date. Updating git repository /casa/host/src/brainrat/brainrat-private/master $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' Using BioProj credentials stored in svn.secret (username 'brainvisa-admin') $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Already up to date. Updating git repository /casa/host/src/brainrat/primatologist-gpl/master $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' Using BioProj credentials stored in svn.secret (username 'brainvisa-admin') $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Already up to date. Updating git repository /casa/host/src/brainvisa-share/master $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Already up to date. Updating git repository /casa/host/src/brainvisa-spm/master $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Already up to date. Updating git repository /casa/host/src/capsul/master $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Already up to date. $ pre-commit install pre-commit installed at .git/hooks/pre-commit Updating git repository /casa/host/src/constellation/constellation-gpl/master $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Already up to date. Updating git repository /casa/host/src/constellation/constellation-nonfree/master $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Already up to date. Updating git repository /casa/host/src/cortical_surface/brainvisa_freesurfer/master $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Already up to date. Updating git repository /casa/host/src/cortical_surface/cortical_surface-gpl/master $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Already up to date. Updating git repository /casa/host/src/cortical_surface/cortical_surface-nonfree/master $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Already up to date. Updating git repository /casa/host/src/development/brainvisa-cmake/master $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Already up to date. $ pre-commit install pre-commit installed at .git/hooks/pre-commit Updating git repository /casa/host/src/development/casa-distro/master $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Already up to date. $ pre-commit install pre-commit installed at .git/hooks/pre-commit Updating git repository /casa/host/src/development/neuro-forge/master $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' $ git update-ref --no-deref refs/bv_head refs/remotes/origin/main $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Already up to date. Updating git repository /casa/host/src/disco/master $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' Using BioProj credentials stored in svn.secret (username 'brainvisa-admin') $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Already up to date. $ pre-commit install pre-commit installed at .git/hooks/pre-commit Updating git repository /casa/host/src/highres-cortex/master $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Already up to date. $ pre-commit install pre-commit installed at .git/hooks/pre-commit Updating git repository /casa/host/src/morphologist/morpho-deepsulci/master $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Already up to date. Updating git repository /casa/host/src/morphologist/morphologist-gpl/master $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' From https://github.com/brainvisa/morphologist-gpl f7d4b001..08ae04dc master -> origin/master $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Updating f7d4b001..08ae04dc Fast-forward .../processes/morphologist_qc_table.py | 2 +- .../processes/morphometry/brainvolumes.py | 15 +- .../processes/morphometry/morpho_report.py | 226 +++++++++++---------- .../morphologist/morpho_bids_hierarchy.py | 9 +- python/morphologist/qc/global_qc_table.py | 21 +- share/foms/morphologist-bids-2.0.json | 20 +- 6 files changed, 169 insertions(+), 124 deletions(-) Updating git repository /casa/host/src/morphologist/morphologist-nonfree/master $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Already up to date. Updating git repository /casa/host/src/morphologist/morphologist-ui/master $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Already up to date. Updating git repository /casa/host/src/morphologist/sulci-nonfree/master $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Already up to date. Updating git repository /casa/host/src/populse/populse_db/master $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Already up to date. $ pre-commit install pre-commit installed at .git/hooks/pre-commit Updating git repository /casa/host/src/soma/soma-base/master $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Already up to date. $ pre-commit install pre-commit installed at .git/hooks/pre-commit Updating git repository /casa/host/src/soma/soma-io/master $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Already up to date. Updating git repository /casa/host/src/soma/soma-workflow/master $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Already up to date. $ pre-commit install pre-commit installed at .git/hooks/pre-commit Summary of Git repositories in /casa/host/src ============================================= ┌───── * uncommitted working tree changes │┌──── + uncommitted index changes ││┌─── $ stash present │││┌── % untracked files ││││ ┌ HEAD ││││ │ ┌ update status ││││ │ │ ┌ bv_maker upstream state ││││ │ │ │ ┌ Git upstream state ││││ │ │ │ │┌ Directory master (65ee945f) ✓ U= aims/aims-free/master master (87e39e9) ✓ U= aims/aims-gpl/master master (540f71ca) ✓ U= anatomist/anatomist-free/master master (eb30f92) ✓ U= anatomist/anatomist-gpl/master master (783981c6) ✓ U= axon/master master (1efaef3) ✓ U= brainrat/bioprocessing/master master (863e579) ✓ U= brainrat/brainrat-gpl/master master (20f9016) ✓ U= brainrat/brainrat-private/master master (c0d8b66) ✓ U= brainrat/primatologist-gpl/master master (bffc425) ✓ U= brainvisa-share/master master (e77cda3) ✓ U= brainvisa-spm/master master (14abfc1a) ✓ U= capsul/master master (5bb66e6) ✓ U= constellation/constellation-gpl/master master (ccb3558) ✓ U= constellation/constellation-nonfree/master master (80716f7) ✓ U= cortical_surface/brainvisa_freesurfer/master master (0ac8a75) ✓ U= cortical_surface/cortical_surface-gpl/master master (c20dd90) ✓ U= cortical_surface/cortical_surface-nonfree/master master (fd12faa) ✓ U= development/brainvisa-cmake/master master (8b568c0) ✓ U= development/casa-distro/master main (8e7e630) ✓ U= development/neuro-forge/master master (e28a829) ✓ U= disco/master master (4bb7822) ✓ U= highres-cortex/master master (e72510d) ✓ U= morphologist/morpho-deepsulci/master master (08ae04dc) ✓ U= morphologist/morphologist-gpl/master master (e3268f3) ✓ U= morphologist/morphologist-nonfree/master master (c22bab8) ✓ U= morphologist/morphologist-ui/master master (cb2e0eb) ✓ U= morphologist/sulci-nonfree/master master (082932e) ✓ U= populse/populse_db/master master (770321e) ✓ U= soma/soma-base/master master (edd62eb) ✓ U= soma/soma-io/master master (24f82c9) ✓ U= soma/soma-workflow/master bv_maker summary: OK step sources: /casa/host/src, started: 2025/11/24 05:04, stopped: 2025/11/24 05:05 All went good. Finished: SUCCESS