Regenerate and upload MNI PD JSONLD files

[surchs]

Once

• [ENH] Update bagel columns nipoppy/nipoppy#354 is merged,

we need to regenerate derivative files for:

• QPN - non-agg
• PPMI - agg
• Calgary - agg (and on CC)

steps:

• pull the latest (latest) version of the CLI with docker pull neurobagel/bagel-cli:latest / singularity pull bagel.sif docker://neurobagel/bagelcli
• regenerate the processing status files with nipoppy
• rerun the CLI (all 3 steps: pheno, bids, derivatives)

and collect feedback (if any) from the nipoppy folks

Next,

• Upload the new .jsonld files into graph databases:
  • PPMI
  • QPN
  • Calgary

Outcomes:

• Two new nodes on BIC:
  • McConnell Brain Imaging Centre - Aggregated (containing PPMI, Calgary)
    • recipe location: ~/dataplace/projects/bic_internal_nodes/closed
    • data location: ~/dataplace/data/bic_internal/closed
  • McConnell Brain Imaging Centre - Open (containing QPN)
    • recipe location: ~/dataplace/projects/bic_internal_nodes/open
    • data location: ~/dataplace/data/bic_internal/open

[surchs]

@michellewang and @mathdugre, these are the steps we need for our PD node

[surchs]

The latest bagelcli is neurobagel/bagelcli:v0.3.3: https://hub.docker.com/repository/docker/neurobagel/bagelcli/tags

Also: here are our docs that have the steps on running the CLI: https://neurobagel.org/cli/#running-the-cli

[alyssadai]

Hey @nikhil153, would you have capacity to regenerate the Neurobagel JSONLD file for the QPN following this issue?

Edit: Done

[alyssadai]

Tasks are now complete - I updated the iss description with the final node names and locations on fairmount.