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TemplateFlow Archive

RRID:SCR_021876 Update Archive

This repository corresponds to the DataLad super-dataset of the TemplateFlow infrastructure. Therefore, this repository indexes actual template datasets (Git repositories), that are linked as Git submodules. This repository is the right place to send issues affecting the whole infrastructure. It is automatically managed via GitHub Actions.

About

Reference anatomies of the brain and corresponding atlases play a central role in experimental neuroimaging workflows and are the foundation for reporting standardized results. The choice of such references —i.e., templates— and atlases is one relevant source of methodological variability across studies, which has recently been brought to attention as an important challenge to reproducibility in neuroscience. TemplateFlow is a publicly available framework for human and nonhuman brain models. The framework combines an open database with software for access, management, and vetting, allowing scientists to distribute their resources under FAIR —findable, accessible, interoperable, reusable— principles. TemplateFlow supports a multifaceted insight into brains across species, and enables multiverse analyses testing whether results generalize across standard references, scales, and in the long term, species, thereby contributing to increasing the reliability of neuroimaging results.

Please visit www.templateflow.org for a more comprehensive description of this project. News and some discussions take place at the Nipy discourse platform.

Vision

The rationale behind TemplateFlow and how we envision it as a fundamental instrument to neuroimaging studies is presented in our preprint:

Ciric R. et al., 2021. doi:10.1101/2021.02.10.430678

Acknowledgments

This work is steered and maintained by the NiPreps Community. The development of this framework is supported the NIMH (RF1MH121867, RAP, OE).

Thanks to the DataLad developers, as we rely on their wonderful tool for the management of the TemplateFlow Archive.

actions-template's People

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actions-template's Issues

Errors in update script

2022-01-11T10:00:07.2110701Z # github.com:22 SSH-2.0-babeld-d2b829ee
2022-01-11T10:00:07.2875825Z Agent pid 16
2022-01-11T10:00:07.2952838Z Identity added: (stdin) ((stdin))
2022-01-11T10:00:07.2954826Z Installing TemplateFlow Archive super-dataset ...
2022-01-11T10:00:07.4989743Z [INFO] Cloning dataset to Dataset(/github/workspace/templateflow) 
2022-01-11T10:00:07.4991878Z [INFO] Attempting to clone from [email protected]:templateflow/templateflow.git to /github/workspace/templateflow 
2022-01-11T10:00:08.1086830Z [INFO] Start enumerating objects 
2022-01-11T10:00:08.1198294Z [INFO] Start counting objects 
2022-01-11T10:00:08.1322719Z [INFO] Start compressing objects 
2022-01-11T10:00:08.1517801Z [INFO] Start receiving objects 
2022-01-11T10:00:08.1938253Z [INFO] Start resolving deltas 
2022-01-11T10:00:08.2212651Z [INFO] Completed clone attempts for Dataset(/github/workspace/templateflow) 
2022-01-11T10:00:08.4178654Z [INFO] Unable to parse git config from origin 
2022-01-11T10:00:08.8846646Z [INFO] Remote origin does not have git-annex installed; setting annex-ignore 
2022-01-11T10:00:08.8856452Z [INFO] This could be a problem with the git-annex installation on the remote. Please make sure that git-annex-shell is available in PATH when you ssh into the remote. Once you have fixed the git-annex installation, run: git annex enableremote origin 
2022-01-11T10:00:08.9236367Z [INFO] access to 1 dataset sibling public-s3 not auto-enabled, enable with:
2022-01-11T10:00:08.9239522Z | 		datalad siblings -d "/github/workspace/templateflow" enable -s public-s3 
2022-01-11T10:00:08.9255659Z install(ok): /github/workspace/templateflow (dataset)
2022-01-11T10:00:08.9616488Z Installing template tpl-RESILIENT ...
2022-01-11T10:00:09.2069968Z [INFO] Cloning dataset to Dataset(/github/workspace/templateflow/tpl-RESILIENT) 
2022-01-11T10:00:09.2072082Z [INFO] Attempting to clone from [email protected]:templateflow/templateflow.git/tpl-RESILIENT to /github/workspace/templateflow/tpl-RESILIENT 
2022-01-11T10:00:09.6193200Z [INFO] Attempting to clone from https://github.com/templateflow/tpl-RESILIENT.git to /github/workspace/templateflow/tpl-RESILIENT 
2022-01-11T10:00:09.8716226Z [INFO] Start enumerating objects 
2022-01-11T10:00:09.8724232Z [INFO] Start counting objects 
2022-01-11T10:00:09.8758764Z [INFO] Start compressing objects 
2022-01-11T10:00:09.8811849Z [INFO] Start receiving objects 
2022-01-11T10:00:09.8925278Z [INFO] Start resolving deltas 
2022-01-11T10:00:09.9019257Z [INFO] Completed clone attempts for Dataset(/github/workspace/templateflow/tpl-RESILIENT) 
2022-01-11T10:00:10.2669633Z [INFO] Remote origin not usable by git-annex; setting annex-ignore 
2022-01-11T10:00:10.2713435Z [INFO] https://github.com/templateflow/tpl-RESILIENT.git/config download failed: Not Found 
2022-01-11T10:00:11.2879037Z [INFO] Reset branch 'master' to 776f4a6c (from 8e11fcf1) to avoid a detached HEAD 
2022-01-11T10:00:11.3095523Z install(ok): /github/workspace/templateflow/tpl-RESILIENT (dataset) [Installed subdataset in order to get /github/workspace/templateflow/tpl-RESILIENT]
2022-01-11T10:00:11.3467986Z Updating template tpl-RESILIENT ...
2022-01-11T10:00:11.4951655Z [WARNING] path constraints for subdataset updates ignored, because `recursive` option was not given 
2022-01-11T10:00:11.5084583Z [INFO] Fetching updates for Dataset(/github/workspace/templateflow/tpl-RESILIENT) 
2022-01-11T10:00:11.5086651Z [INFO] Start fetching remotes for AnnexRepo(/github/workspace/templateflow/tpl-RESILIENT) 
2022-01-11T10:00:11.5087913Z [INFO] Fetching remote origin 
2022-01-11T10:00:11.6723922Z [INFO] Fetching remote gin-src 
2022-01-11T10:00:12.1364304Z [INFO] Finished fetching remotes for AnnexRepo(/github/workspace/templateflow/tpl-RESILIENT) 
2022-01-11T10:00:12.2648779Z merge(ok): . (dataset) [Merged origin/master]
2022-01-11T10:00:12.2649733Z update(ok): . (dataset)
2022-01-11T10:00:12.2650511Z action summary:
2022-01-11T10:00:12.2651264Z   merge (ok: 1)
2022-01-11T10:00:12.2651989Z   update (ok: 1)
2022-01-11T10:00:12.2884818Z Configuring g-Node/GIN remote ...
2022-01-11T10:00:12.2886208Z /github/workspace/templateflow/tpl-RESILIENT /github/workspace/templateflow
2022-01-11T10:00:15.8147075Z .: gin(+) [https://gin.g-node.org/templateflow/tpl-RESILIENT (git)]
2022-01-11T10:00:16.0624149Z [ERROR] Could not deduce RI type for None [network.py:__new__:423] (ValueError) 
2022-01-11T10:00:16.3138582Z Pushing to g-Node/GIN ...
2022-01-11T10:00:16.4759895Z [INFO] Determine push target 
2022-01-11T10:00:16.4765908Z [INFO] Push refspecs 
2022-01-11T10:00:17.0268807Z Host key verification failed.
2022-01-11T10:00:17.0366116Z [INFO] Transfer data 
2022-01-11T10:00:17.2060278Z [INFO] Update availability information 
2022-01-11T10:00:17.8179924Z CommandError: 'git -c diff.ignoreSubmodules=none -c [email protected]:/templateflow/tpl-RESILIENT.git.insteadof=https://gin.g-node.org/templateflow/tpl-RESILIENT fetch gin git-annex' failed with exitcode 128 under /github/workspace/templateflow/tpl-RESILIENT
2022-01-11T10:00:17.8182211Z Host key verification failed.
2022-01-11T10:00:17.8184557Z ConnectionOpenFailedError: 'ssh -fN -o ControlMaster=auto -o ControlPersist=15m -o ControlPath=/github/home/.cache/datalad/sockets/04ae1e9d [email protected]' failed with exitcode 255 [Failed to open SSH connection (could not start ControlMaster process)]
2022-01-11T10:00:17.8186870Z fatal: Could not read from remote repository.
2022-01-11T10:00:17.8187455Z 
2022-01-11T10:00:17.8188259Z Please make sure you have the correct access rights
2022-01-11T10:00:17.8189217Z and the repository exists.
2022-01-11T10:00:17.8422006Z Pushing to GitHub ...
2022-01-11T10:00:18.0053908Z [INFO] Determine push target 
2022-01-11T10:00:18.0058090Z [INFO] Push refspecs 
2022-01-11T10:00:18.1017200Z [INFO] Transfer data 
2022-01-11T10:00:18.1018216Z [INFO] Update availability information 
2022-01-11T10:00:18.4038449Z CommandError: 'git -c diff.ignoreSubmodules=none push --progress --porcelain origin master git-annex:git-annex' failed with exitcode 128 under /github/workspace/templateflow/tpl-RESILIENT
2022-01-11T10:00:18.4041009Z fatal: could not read Username for 'https://github.com': No such device or address
2022-01-11T10:00:18.4284800Z Pushing super-dataset ...
2022-01-11T10:00:18.4285923Z /github/workspace/templateflow
2022-01-11T10:00:19.1539317Z add(ok): tpl-RESILIENT (file)
2022-01-11T10:00:19.1540400Z save(ok): . (dataset)
2022-01-11T10:00:19.1541536Z action summary:
2022-01-11T10:00:19.1542367Z   add (ok: 1)
2022-01-11T10:00:19.1543148Z   save (ok: 1)
2022-01-11T10:00:19.3395832Z [INFO] Determine push target 
2022-01-11T10:00:19.3403127Z [INFO] Push refspecs 
2022-01-11T10:00:19.9129590Z [INFO] Transfer data 
2022-01-11T10:00:19.9130620Z [INFO] Update availability information 
2022-01-11T10:00:20.7101579Z [INFO] Start enumerating objects 
2022-01-11T10:00:20.7108044Z [INFO] Start counting objects 
2022-01-11T10:00:20.7116941Z [INFO] Start compressing objects 
2022-01-11T10:00:20.7123657Z [INFO] Start writing objects 
2022-01-11T10:00:20.7603400Z [INFO] Start resolving deltas 
2022-01-11T10:00:21.0446071Z [INFO] Finished 
2022-01-11T10:00:21.0457450Z [INFO] Finished push of Dataset(/github/workspace/templateflow) 
2022-01-11T10:00:21.0463310Z publish(ok): . (dataset) [refs/heads/git-annex->origin:refs/heads/git-annex d45a637..e22b16f]
2022-01-11T10:00:21.0465014Z publish(ok): . (dataset) [refs/heads/master->origin:refs/heads/master dafec50..3321e07]
2022-01-11T10:00:21.0762451Z Exporting to S3 bucket ...
2022-01-11T10:00:21.3402688Z .: s3(?) [git]
2022-01-11T10:00:21.3642299Z /github/workspace/templateflow/tpl-RESILIENT /github/workspace/templateflow
2022-01-11T10:00:21.5700774Z [INFO] Installing Dataset(/github/workspace/templateflow/tpl-RESILIENT) to get /github/workspace/templateflow/tpl-RESILIENT/cohort-1 recursively 
2022-01-11T10:00:21.5723133Z [INFO] Installing Dataset(/github/workspace/templateflow/tpl-RESILIENT) to get /github/workspace/templateflow/tpl-RESILIENT/cohort-4 recursively 
2022-01-11T10:00:21.5756404Z [INFO] Installing Dataset(/github/workspace/templateflow/tpl-RESILIENT) to get /github/workspace/templateflow/tpl-RESILIENT/cohort-2 recursively 
2022-01-11T10:00:21.5779134Z [INFO] Installing Dataset(/github/workspace/templateflow/tpl-RESILIENT) to get /github/workspace/templateflow/tpl-RESILIENT/cohort-3 recursively 
2022-01-11T10:01:10.3471506Z get(ok): cohort-1/tpl-RESILIENT_cohort-1_T1w.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3473568Z get(ok): cohort-1/tpl-RESILIENT_cohort-1_atlas-WHS_desc-Cerebrum3TissueLabels_dseg.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3475514Z get(ok): cohort-1/tpl-RESILIENT_cohort-1_desc-CSF_probseg.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3483627Z get(ok): cohort-1/tpl-RESILIENT_cohort-1_desc-GM_probseg.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3485660Z get(ok): cohort-1/tpl-RESILIENT_cohort-1_desc-WM_probseg.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3487518Z get(ok): cohort-1/tpl-RESILIENT_cohort-1_desc-brain_T1w.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3489831Z get(ok): cohort-1/tpl-RESILIENT_cohort-1_desc-brain_mask.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3491544Z get(ok): cohort-2/tpl-RESILIENT_cohort-2_T1w.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3493873Z get(ok): cohort-2/tpl-RESILIENT_cohort-2_atlas-WHS_desc-Cerebrum3TissueLabels_dseg.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3495936Z get(ok): cohort-2/tpl-RESILIENT_cohort-2_desc-CSF_probseg.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3497796Z get(ok): cohort-2/tpl-RESILIENT_cohort-2_desc-GM_probseg.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3499620Z get(ok): cohort-2/tpl-RESILIENT_cohort-2_desc-WM_probseg.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3501441Z get(ok): cohort-2/tpl-RESILIENT_cohort-2_desc-brain_T1w.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3503232Z get(ok): cohort-2/tpl-RESILIENT_cohort-2_desc-brain_mask.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3506405Z get(ok): cohort-4/tpl-RESILIENT_cohort-4_T1w.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3508269Z get(ok): cohort-4/tpl-RESILIENT_cohort-4_atlas-WHS_desc-Cerebrum3TissueLabels_dseg.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3510165Z get(ok): cohort-4/tpl-RESILIENT_cohort-4_desc-CSF_probseg.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3511867Z get(ok): cohort-4/tpl-RESILIENT_cohort-4_desc-GM_probseg.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3513706Z get(ok): cohort-4/tpl-RESILIENT_cohort-4_desc-WM_probseg.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3515374Z get(ok): cohort-4/tpl-RESILIENT_cohort-4_desc-brain_T1w.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3517024Z get(ok): cohort-4/tpl-RESILIENT_cohort-4_desc-brain_mask.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3518556Z get(ok): cohort-3/tpl-RESILIENT_cohort-3_T1w.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3520399Z get(ok): cohort-3/tpl-RESILIENT_cohort-3_atlas-WHS_desc-Cerebrum3TissueLabels_dseg.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3522286Z get(ok): cohort-3/tpl-RESILIENT_cohort-3_desc-CSF_probseg.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3523955Z get(ok): cohort-3/tpl-RESILIENT_cohort-3_desc-GM_probseg.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3525632Z get(ok): cohort-3/tpl-RESILIENT_cohort-3_desc-WM_probseg.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3527269Z get(ok): cohort-3/tpl-RESILIENT_cohort-3_desc-brain_T1w.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3529266Z get(ok): cohort-3/tpl-RESILIENT_cohort-3_desc-brain_mask.nii.gz (file) [from gin-src...]
2022-01-11T10:01:10.3530568Z get(ok): cohort-1 (directory)
2022-01-11T10:01:10.3531530Z get(ok): cohort-2 (directory)
2022-01-11T10:01:10.3532476Z get(ok): cohort-4 (directory)
2022-01-11T10:01:10.3533434Z get(ok): cohort-3 (directory)
2022-01-11T10:01:10.3534221Z action summary:
2022-01-11T10:01:10.3534998Z   get (notneeded: 2, ok: 32)
2022-01-11T10:01:10.4504117Z   Set both AWS_ACCESS_KEY_ID and AWS_SECRET_ACCESS_KEY to use S3
2022-01-11T10:01:10.4505284Z unexport s3 template_description.json 
2022-01-11T10:01:10.4506580Z failed
2022-01-11T10:01:10.5920691Z export s3 .datalad/.gitattributes ok
2022-01-11T10:01:10.6138665Z export s3 .datalad/config ok
2022-01-11T10:01:10.6359721Z export s3 .gitattributes ok
2022-01-11T10:01:10.6532299Z export s3 .github/workflows/update-superdataset.yml ok
2022-01-11T10:01:10.6720267Z export s3 LICENSE ok
2022-01-11T10:01:10.6908522Z export s3 cohort-1/tpl-RESILIENT_cohort-1_T1w.nii.gz ok
2022-01-11T10:01:10.7138210Z export s3 cohort-1/tpl-RESILIENT_cohort-1_atlas-WHS_desc-Cerebrum3TissueLabels_dseg.nii.gz ok
2022-01-11T10:01:10.7323382Z export s3 cohort-1/tpl-RESILIENT_cohort-1_desc-CSF_probseg.nii.gz ok
2022-01-11T10:01:10.7500965Z export s3 cohort-1/tpl-RESILIENT_cohort-1_desc-GM_probseg.nii.gz ok
2022-01-11T10:01:10.7706206Z export s3 cohort-1/tpl-RESILIENT_cohort-1_desc-WM_probseg.nii.gz ok
2022-01-11T10:01:10.7904963Z export s3 cohort-1/tpl-RESILIENT_cohort-1_desc-brain_T1w.nii.gz ok
2022-01-11T10:01:10.8081949Z export s3 cohort-1/tpl-RESILIENT_cohort-1_desc-brain_mask.nii.gz ok
2022-01-11T10:01:10.8270461Z export s3 cohort-2/tpl-RESILIENT_cohort-2_T1w.nii.gz ok
2022-01-11T10:01:10.8469561Z export s3 cohort-2/tpl-RESILIENT_cohort-2_atlas-WHS_desc-Cerebrum3TissueLabels_dseg.nii.gz ok
2022-01-11T10:01:10.8640272Z export s3 cohort-2/tpl-RESILIENT_cohort-2_desc-CSF_probseg.nii.gz ok
2022-01-11T10:01:10.8834516Z export s3 cohort-2/tpl-RESILIENT_cohort-2_desc-GM_probseg.nii.gz ok
2022-01-11T10:01:10.9037333Z export s3 cohort-2/tpl-RESILIENT_cohort-2_desc-WM_probseg.nii.gz ok
2022-01-11T10:01:10.9226817Z export s3 cohort-2/tpl-RESILIENT_cohort-2_desc-brain_T1w.nii.gz ok
2022-01-11T10:01:10.9420451Z export s3 cohort-2/tpl-RESILIENT_cohort-2_desc-brain_mask.nii.gz ok
2022-01-11T10:01:10.9629634Z export s3 cohort-3/tpl-RESILIENT_cohort-3_T1w.nii.gz ok
2022-01-11T10:01:10.9813594Z export s3 cohort-3/tpl-RESILIENT_cohort-3_atlas-WHS_desc-Cerebrum3TissueLabels_dseg.nii.gz ok
2022-01-11T10:01:11.0005282Z export s3 cohort-3/tpl-RESILIENT_cohort-3_desc-CSF_probseg.nii.gz ok
2022-01-11T10:01:11.0182650Z export s3 cohort-3/tpl-RESILIENT_cohort-3_desc-GM_probseg.nii.gz ok
2022-01-11T10:01:11.0373811Z export s3 cohort-3/tpl-RESILIENT_cohort-3_desc-WM_probseg.nii.gz ok
2022-01-11T10:01:11.0639476Z export s3 cohort-3/tpl-RESILIENT_cohort-3_desc-brain_T1w.nii.gz ok
2022-01-11T10:01:11.0812388Z export s3 cohort-3/tpl-RESILIENT_cohort-3_desc-brain_mask.nii.gz ok
2022-01-11T10:01:11.0993694Z export s3 cohort-4/tpl-RESILIENT_cohort-4_T1w.nii.gz ok
2022-01-11T10:01:11.1189594Z export s3 cohort-4/tpl-RESILIENT_cohort-4_atlas-WHS_desc-Cerebrum3TissueLabels_dseg.nii.gz ok
2022-01-11T10:01:11.1365474Z export s3 cohort-4/tpl-RESILIENT_cohort-4_desc-CSF_probseg.nii.gz ok
2022-01-11T10:01:11.1531792Z export s3 cohort-4/tpl-RESILIENT_cohort-4_desc-GM_probseg.nii.gz ok
2022-01-11T10:01:11.1695269Z export s3 cohort-4/tpl-RESILIENT_cohort-4_desc-WM_probseg.nii.gz ok
2022-01-11T10:01:11.1999317Z export s3 cohort-4/tpl-RESILIENT_cohort-4_desc-brain_T1w.nii.gz ok
2022-01-11T10:01:11.2176213Z export s3 cohort-4/tpl-RESILIENT_cohort-4_desc-brain_mask.nii.gz ok
2022-01-11T10:01:11.2350110Z export s3 template_description.json ok
2022-01-11T10:01:11.2502044Z (recording state in git...)
2022-01-11T10:01:11.2583808Z export: 1 failed
2022-01-11T10:01:11.2739091Z /github/workspace/templateflow

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