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Update (neuro)docker image #81
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yarikoptic
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…from neurodesk fsl recipe failed with FSL installation failure ERROR occurred during installation! This command returned an error: /opt/fsl-6.0.6.4/bin/conda env update -p /opt/fsl-6.0.6.4 -f /tmp/tmp_ynzfnbz/fsl-6.0.6.4_linux-64.yml
….16.5), nobrainer, ...
note that apparently there is no credentials added for docker pushes so no attempt to build even made.
I will reorder commands so we could see if it at least builds ok etc. |
This was referenced Jun 12, 2024
Otherwise if no t1w files found, the variable t1w would not get populated in the loop at all and cause the crash. But it also does not make much sense to return only the last hit in the loop. Checking the workflow, it seems outputs are not used at all anyways, so we are gonna try to return a list
…, deno bids validator
* gh-yarikoptic/bfs: Return lists of defaced t1w and t2w and define it for t2w [DATALAD RUNCMD] run codespell throughout fixing typo automagically [DATALAD RUNCMD] Fix bidsonym/run_deeid.py brainextration typo which triggered this all [DATALAD RUNCMD] Do interactive fixing of typos [DATALAD RUNCMD] run codespell throughout fixing typo automagically Add rudimentary codespell config Add github action to codespell master on push and PRs
* gh-yarikoptic/bfs: BF: more of defining defaults to not cause obnoxious crashes
I am done with this as far I consider it done. Includes fixes from |
@PeerHerholz please review&merge! |
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not even know if bidsonym is still worth (re)trying on my dataset but can't reliably do it without getting a container ;-) hence decided to possibly duplicate efforts with @Remi-Gau of
and see the container built.
If finished, closes #79
Ideally
deno
into recipe to be installed in conda, so then we could install new schema-based validator therecurrent gotchas
/neurodocker/startup.sh
in docker recipes, in effect ignores neurodocker/templates/_header.yaml? ReproNim/neurodocker#620 - worked around, seems to be working just fine