Manage Nipoppy neuroimaging dataset workflows from initialization to extraction.
npx skills add https://github.com/bcmcpher/my-skills --skill nipoppy-cli
Please help me install this Agent Skill. Skill: nipoppy-cli Source: https://github.com/bcmcpher/my-skills/tree/main/plugins/nipoppy-cli/skills/nipoppy-cli Command: npx skills add https://github.com/bcmcpher/my-skills --skill nipoppy-cli
Nipoppy CLI helps researchers manage and automate complex neuroimaging data workflows in a single, consistent interface, reducing manual setup and error-prone steps.
Run nipoppy init /data/my-study to scaffold a new Nipoppy dataset, then follow with manifest edits and subsequent commands in the typical linear workflow.
High-intent search queries and answers about installing and using this skill.
To manage neuroimaging workflows, initialize a new dataset with a scaffold command, edit the manifest, register participants, and execute subsequent commands linearly to handle curation, BIDS conversion, processing, and extraction.
Running neuroimaging workflows in Linux with Apptainer requires valid dataset states, specifically a config.json file and manifest.tsv, alongside Boutiques descriptors to validate inputs and execute pipeline commands safely.
BIDS conversion for neuroimaging datasets works by running a bidsify command after dataset reorganization, utilizing dataset-state checks to ensure proper configuration before executing the conversion pipeline safely.
The best way to track neuroimaging data curation status is by using a centralized CLI workflow that applies dataset-state checks against a manifest, ensuring consistent validation and reducing configuration errors.
Yes, you can extract imaging-derived phenotypes immediately after processing neuroimaging pipelines, as the workflow supports end-to-end extraction as the final step in the standard linear dataset pipeline.
bcmcpherGenerate Boutiques schema 0.5 JSON descriptors from CLI help output.
Lord1EgyptOrganize and validate neuroscience data according to the BIDS specification.
tassiovaleOrganize, query, validate, and convert neuroscience data into BIDS-compliant datasets.
zongtingweiSegment cells, phenotype them, and summarize spatial patterns in imaging mass cytometry data.
