{"slug":"k-dense-ai-bids","name":"bids","description":"Use this skill when working with Brain Imaging Data Structure (BIDS) datasets: organizing neuroscience and biomedical data (MRI, EEG, MEG, iEEG, PET, microscopy, NIRS, motion capture, EMG, MR spectroscopy, behavioral), querying BIDS layouts, validating compliance, converting DICOM to BIDS, writing metadata sidecars, or creating BIDS derivatives.","long_description":"---\nname: bids\ndescription: >\n  Use this skill when working with Brain Imaging Data Structure (BIDS) datasets:\n  organizing neuroscience and biomedical data (MRI, EEG, MEG, iEEG, PET, microscopy,\n  NIRS, motion capture, EMG, MR spectroscopy, behavioral), querying BIDS layouts,\n  validating compliance, converting DICOM to BIDS, writing metadata sidecars, or\n  creating BIDS derivatives.\nlicense: https://creativecommons.org/licenses/by/4.0/\nmetadata:\n  version: \"1.1\"\n  skill-author: Yaroslav Halchenko\n---\n\n# Brain Imaging Data Structure (BIDS)\n\n## Overview\n\nThe Brain Imaging Data Structure (BIDS) is a community standard for organizing and describing neuroscience and biomedical research datasets. It defines a consistent file naming convention, directory hierarchy, and metadata schema so that datasets are immediately understandable by humans and software tools alike. BIDS is governed by the BIDS Specification (currently v1.11.x) and is maintained by the community via the BIDS-Standard GitHub organization.\n\nWhile BIDS originated for MRI, it has grown well beyond neuroimaging. The specification now covers 11 modalities spanning imaging, electrophysiology, and behavioral data:\n\n- **Imaging**: MRI (structural, functional, diffusion, fieldmaps, perfusion/ASL), PET, microscopy\n- **Electrophysiology**: EEG, MEG, iEEG (intracranial EEG), EMG\n- **Other**: NIRS (near-infrared spectroscopy), motion capture, behavioral data (without imaging), MR spectroscopy\n\nActive BEPs are extending BIDS further — notably BEP032 (microelectrode electrophysiology) will add support for extracellular recordings including Neuropixels probes, bringing BIDS to a prevalent methodology in animal neuroscience research (see also the neuropixels-analysis skill).\n\nAdoption is required or strongly encouraged by major data repositories (OpenNeuro, DANDI), leading journals (NeuroImage, Human Brain Mapping, Scientific Data), and funding agencies (NIH, ERC).\n\nThe Python ecosystem for BIDS centers on **PyBIDS** (`pybids`) for querying and indexing BIDS datasets, and the **bids-validator** (Deno-based, available as PyPI package `bids-validator-deno` or via Deno directly) for compliance checking. Conversion from DICOM is typically done with **HeuDiConv**, **dcm2bids**, or **BIDScoin**.\n\n## When to Use This Skill\n\nApply this skill when:\n- Organizing raw neuroscience data (imaging, electrophysiology, behavioral) into BIDS-compliant directory structures\n- Querying an existing BIDS dataset to find specific files by subject, session, task, run, or modality\n- Validating a dataset against the BIDS specification before sharing or submission\n- Converting DICOM data from scanners into BIDS format\n- Writing or editing JSON sidecar metadata files\n- Creating BIDS-compliant derivatives (preprocessed data, analysis outputs)\n- Setting up a `dataset_description.json` for a new dataset\n- Working with BIDS entities (subject, session, task, acquisition, run, etc.)\n- Configuring `.bidsignore` to exclude files from validation\n- Preparing data for upload to OpenNeuro, DANDI, or other BIDS-aware repositories\n\n## Installation\n\n```bash\n# Core BIDS querying library\nuv pip install pybids\n\n# BIDS validator (Deno-based, installed via PyPI wrapper)\nuv pip install bids-validator-deno\n# Alternative: install directly via Deno\n# deno install -g -A npm:bids-validator\n\n# DICOM-to-BIDS converters (install as needed)\nuv pip install heudiconv       # HeuDiConv - heuristic-based DICOM conversion\nuv pip install dcm2bids        # dcm2bids - config-file-based conversion\n# BIDScoin: uv pip install bidscoin\n\n# Useful companions\nuv pip install nibabel          # NIfTI/other neuroimaging file I/O\nuv pip install pydicom          # DICOM file reading (used by converters)\n```\n\n## Core Workflows\n\nTwelve workflow areas, each with worked code, are documented in\n[references/core_workflows.md](references/core_workflows.md):\n\n1. **BIDS directory structure** — the required layout and where each modality belongs.\n2. **`dataset_description.json`** — the required fields and how to generate it.\n3. **Querying with PyBIDS** — `BIDSLayout`, entity filters, sidecar metadata with\n   automatic inheritance, and building paths from entities.\n4. **Validation** — `bids-validator` via the PyPI wrapper (recommended), via Deno\n   directly, the legacy Node validator, and using `.bidsignore` to exclude files.\n5. **Entities and file naming** — the entity order and naming grammar.\n6. **DICOM to BIDS conversion** — HeuDiConv (including the turnkey ReproIn path and the\n   reconnaissance → heuristic → convert sequence) and dcm2bids (config-file based).\n7. **Metadata sidecars** — required and recommended JSON fields per modality.\n8. **Events files** — task fMRI event timing and column conventions.\n9. **Participants file** — `participants.tsv` and its data dictionary.\n10. **Derivatives** — the derivatives layout and its `dataset_description.json`.\n11. **Advanced PyBIDS** — index caching, including derivatives, confound regressors, and\n    DataFrame output.\n12. **BIDS-Apps** — the standard invocation pattern, and fMRIPrep, MRIQC, and QSIPrep.\n\nValidate early and often: PyBIDS validates structure when it indexes a dataset, so an\nindexing failure usually means a naming or metadata problem rather than a code bug.\n\n## Reference Materials\n\nThis skill includes detailed reference documentation:\n\n- **bids_schema.json**: Machine-readable BIDS schema (from https://bids-specification.readthedocs.io/en/stable/schema.json). This is the authoritative source for entity definitions, ordering rules, filename templates, allowed suffixes per datatype, and metadata field requirements. BEP-specific schemas are at https://github.com/bids-standard/bids-schema/tree/main/BEPs.\n- **beps.yml**: Current list of all BIDS Extension Proposals with titles, leads, status, and links (from [bids-website](https://github.com/bids-standard/bids-website/blob/main/data/beps/beps.yml))\n- **bids_specification.md**: Human-readable summary of the entity table, datatype reference, directory structure rules, template spaces, and specification changelog\n- **metadata_fields.md**: Required and recommended JSON sidecar fields for every BIDS modality (anat, func, dwi, fmap, eeg, meg, pet, etc.)\n- **conversion_tools.md**: Detailed workflows for HeuDiConv, dcm2bids, and BIDScoin including heuristic/config examples and troubleshooting\n\nUpdate schema and BEPs with: `python scripts/update_schema.py`\n\n## Common Issues and Solutions\n\n### 1. Validator reports \"Not a BIDS dataset\"\n**Cause**: Missing `dataset_description.json` at the root.\n**Fix**: Create the file with at minimum `{\"Name\": \"...\", \"BIDSVersion\": \"1.10.0\"}`.\n\n### 2. Inconsistent subjects warning\n**Cause**: Not all subjects have the same set of files (some missing sessions, runs, etc.).\n**Fix**: This is a warning, not an error. Use `--ignoreSubjectConsistency` if intentional. Document missing data in `participants.tsv` or a `scans.tsv`.\n\n### 3. Missing SliceTiming\n**Cause**: `dcm2niix` couldn't extract slice timing from DICOM headers.\n**Fix**: Determine slice order from the scan protocol and add manually to the JSON sidecar. Common patterns: ascending, descending, interleaved (odd-first or even-first).\n\n### 4. Phase encoding direction confusion\n**Cause**: Axis labels (i/j/k vs x/y/z vs LR/AP/SI) are confusing.\n**Fix**: In BIDS, use NIfTI image axes: `i`=first axis, `j`=second, `k`=third. `-` means negative direction. For standard axial acquisitions: `j` is typically anterior-posterior. Verify with the acquisition protocol.\n\n### 5. PyBIDS is slow on large datasets\n**Cause**: Full filesystem indexing on every `BIDSLayout()` call.\n**Fix**: Use `database_path` to cache the index to an SQLite file:\n```python\nlayout = BIDSLayout(\"/data\", database_path=\"/data/.pybids_cache.db\")\n```\n\n### 6. Derivatives not found by PyBIDS\n**Cause**: Derivatives directory missing its own `dataset_description.json`.\n**Fix**: Every derivatives directory must have `dataset_description.json` with `\"DatasetType\": \"derivative\"`.\n\n### 7. Events file timing is off\n**Cause**: `onset` times are relative to the wrong reference (e.g., trigger time vs first volume).\n**Fix**: Onsets must be in seconds relative to the first volume of that run's acquisition. Account for dummy scans if they were discarded.\n\n### 8. TSV files fail validation\n**Cause**: Encoding or delimiter issues (spaces instead of tabs, BOM characters, Windows line endings).\n**Fix**: Ensure tab-separated values with UTF-8 encoding and Unix line endings (`\\n`). Use `n/a` (not `NA`, `NaN`, or empty) for missing values.\n\n## Best Practices\n\n1. **Validate early and often** - Run the BIDS validator after every conversion or modification. Fix errors before they compound.\n\n2. **Use metadata inheritance** - Place shared metadata (e.g., `TaskName`, scanner parameters) in top-level sidecar files rather than duplicating in every subject's directory.\n\n3. **Keep sourcedata** - Store the original DICOM (or other raw) data under `sourcedata/` so conversions are reproducible. Add `sourcedata/` to `.bidsignore`.\n\n4. **Use consistent naming from the start** - Define your BIDS naming scheme before data collection. Use the ReproIn naming convention for scan protocols to enable automatic conversion.\n\n5. **Document your dataset** - Write a thorough `README` describing the study design, acquisition parameters, known issues, and any deviations from BIDS.\n\n6. **Use scans.tsv for run-level metadata** - Record per-run acquisition times and quality notes:\n   ```\n   filename\tacq_time\tquality\n   func/sub-01_task-rest_bold.nii.gz\t2025-01-15T10:30:00\tgood\n   ```\n\n7. **Version your dataset** - Use `CHANGES` to document dataset modifications. Consider DataLad for full version control of large datasets.\n\n8. **Deface anatomical images** - Remove facial features from T1w/T2w images before sharing (e.g., using `pydeface`, `mri_deface`, or `afni_refacer`). Store defaced versions as the primary data or use `_defacemask` files.\n\n9. **Use BIDS URIs for provenance** - In derivatives, reference source files using BIDS URIs: `bids::sub-01/anat/sub-01_T1w.nii.gz`.\n\n10. **Prefer community tools** - Use established BIDS-Apps (fMRIPrep, MRIQC, QSIPrep) rather than custom pipelines when possible. They handle BIDS I/O correctly and produce BIDS-compliant derivatives.\n\n11. **Study bids-examples** - The [bids-examples](https://github.com/bids-standard/bids-examples) repository is the canonical collection of prototypical BIDS datasets covering different modalities and use cases (MRI, fMRI, DWI, EEG, MEG, iEEG, PET, ASL, genetics, derivatives, and more). Use it as a reference when structuring your own dataset, as test data for BIDS tools, or to understand how a specific modality should be organized. Each example passes the BIDS validator.\n\n## BIDS Extension Proposals (BEPs)\n\nBEPs are community-driven proposals to extend BIDS to new modalities, derivatives, or metadata. The full list with status, leads, and links is in `references/beps.yml` (fetched from the [bids-website](https://github.com/bids-standard/bids-website/blob/main/data/beps/beps.yml)). BEP-specific schema previews are rendered at https://github.com/bids-standard/bids-schema/tree/main/BEPs.\n\n**Current BEPs** (as of schema update):\n\n| BEP | Title | Content | Status |\n|-----|-------|---------|--------|\n| 004 | Susceptibility Weighted Imaging | raw | Seeking new leader |\n| 011 | Structural preprocessing derivatives | derivative | Has PR (#518) |\n| 012 | Functional preprocessing derivatives | derivative | Has PR (#519), schema implemented |\n| 014 | Affine transforms and nonlinear field warps | derivative | X5 format development |\n| 016 | Diffusion weighted imaging derivatives | derivative | Has PR (#2211) |\n| 017 | Generic BIDS connectivity data schema | derivative | In development |\n| 021 | Common Electrophysiological Derivatives | derivative | In development |\n| 023 | PET Preprocessing derivatives | derivative | In development |\n| 024 | Computed Tomography scan | raw | S","tagline":"Use this skill when working with Brain Imaging Data Structure (BIDS) datasets: organizing neuroscience and biomedical data (MRI, EEG, MEG, iEEG, PET, microscopy, NIRS, motion capture, EMG, MR spectroscopy, behavioral), querying BIDS layouts, validating compliance, converting DICO","category":"security","tags":["agent-skill"],"author":"K-Dense-AI","verified":false,"attribution":{"status":"registry_indexed","statusLabel":"Registry indexed","shortLabel":"REGISTRY INDEXED","sourceLabel":"recursive skill source sync","sourceDetail":"K-Dense-AI/scientific-agent-skills","creatorName":"K-Dense-AI","creatorUrl":"https://github.com/K-Dense-AI","sourceUrl":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/bids","indexedBy":"OpenAgentSkill community index","claimUrl":"https://www.openagentskill.com/skills/k-dense-ai-bids#claim-this-skill","claimCta":"Claim this skill","trustNote":"This listing was indexed from public sources and is not marked official until a maintainer claim is approved.","publicNote":"Attribution links to the public repository or creator profile. 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issue activity unavailable in current metadata"},{"status":"pass","label":"Recent maintenance","detail":"6d since push"},{"status":"pass","label":"License clarity","detail":"https://creativecommons.org/licenses/by/4.0/"},{"status":"pass","label":"README/SKILL.md completeness","detail":"Metadata includes enough usage and workflow context"},{"status":"warn","label":"Dependency/runtime risk","detail":"command execution surface, external package install surface"},{"status":"pass","label":"Install availability","detail":"npx skills add K-Dense-AI/scientific-agent-skills --skill bids"},{"status":"pass","label":"Install command safety","detail":"standard package or runtime install path"},{"status":"warn","label":"Permission surface","detail":"shell or command execution, filesystem or document access"},{"status":"pass","label":"Repository evidence","detail":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/bids"},{"status":"info","label":"Review status","detail":"AI review data available"},{"status":"info","label":"Agent Proven outcomes","detail":"No agent outcome data yet"},{"status":"warn","label":"Ownership","detail":"No approved owner claim yet"},{"status":"pass","label":"OpenAgentSkill usage","detail":"5 views, 0 install copies"},{"status":"info","label":"Agent outcomes","detail":"No agent outcome data yet"}],"strengths":["AI review approved","Install path is available","Repository evidence is available","Recently maintained repository","Large GitHub adoption signal","Install command has no obvious high-risk pattern","Outcome loop is ready but needs first real agent run"],"warnings":["The alternative Deno install command uses `-A` (allow all permissions), which grants excessive permissions to a globally installed script; 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this should be scoped or clearly explained if the agent is expected to run it.","Permission surface needs review: shell or command execution, filesystem or document access","Dependency/runtime risk: command execution surface, external package install surface","Permission surface: shell or command execution, filesystem or document access"]},"outcomeEvidence":{"total":0,"successes":0,"failures":0,"notRelevant":0,"successRate":null,"installAttempts":0,"riskBlocked":0,"setupRequired":0,"installSuccessRate":null,"avgOutputQuality":null,"avgTimeToUsefulMs":null,"productionOutcomes":0,"humanReviewRequired":0,"recentSuccessRate":null,"recentFailureRate":null,"uniqueAgents":0,"agentProvenScore":0,"agentProvenLabel":"Needs first agent run","lastOutcomeAt":null,"label":"No agent outcome data yet"},"autoInstall":{"allowed":false,"sandboxRequired":true,"policy":"human_review_before_install","reason":"Compare alternatives before installing."},"outcome_loop":{"version":"openagentskill-agent-outcome-v4","required_after_install":true,"endpoint":"/api/agent/outcome","method":"POST","event_id_source":"feedback.event_id, install_receipt.resolve_event_id, or decision_packet.outcome_feedback.event_id","expected_outcomes":["success","failed","not_relevant","blocked_by_risk","setup_required"],"required_fields":["event_id","skill_slug","task"],"quality_fields":["task_success","output_quality","error_type","human_review_required","used_in_production","workspace","evidence_url","time_to_useful_ms","source_version"],"ranking_inputs_updated":["Trust Score v5 outcome confidence","Agent Proven Score","Resolve ranking task-fit evidence","Skill detail machine-readable metadata","Outcome leaderboard"]},"agent_contract":{"suited_tasks":["security","agent-skill"],"suited_agents":["Codex","Claude Code","Cursor","OpenAgentSkill CLI"],"install_command":"npx skills add K-Dense-AI/scientific-agent-skills --skill bids","trust_score":67,"trust_version":"trust-score-v5","risk_level":"medium","do_not_use_when":["Production credentials, payments, or irreversible account changes without explicit human review","Sensitive private data before reviewing repository code, license, and permission surface","Automatic installation in a production workspace"],"before_install":["Read the audit page and machine-readable metadata.","Confirm the install command, license, and permission surface fit the workspace.","Get explicit human approval or choose an alternative before installing."],"after_run":["Report the outcome to /api/agent/outcome using the resolve event id.","Include output_quality, workspace, human_review_required, and evidence_url when available.","Re-resolve before broad production rollout."]},"bestFor":["security","agent-skill"],"doNotUseFor":["Production credentials, payments, or irreversible account changes without explicit human review","Sensitive private data before reviewing repository code, license, and permission surface","Automatic installation in a production workspace"],"knownRisks":["The alternative Deno install command uses `-A` (allow all permissions), which grants excessive permissions to a globally installed script; this should be scoped or clearly explained if the agent is expected to run it.","Permission surface needs review: shell or command execution, filesystem or document access","Dependency/runtime risk: command execution surface, external package install surface","Permission surface: shell or command execution, filesystem or document access"],"backward_compatible":{"trust_score_v4":{"version":"trust-score-v4","score":75,"tier":"strong","label":"Strong shortlist","summary":"Good trust signals with a few areas worth checking before rollout."}}},"trust_score_v4":{"version":"trust-score-v4","score":75,"tier":"strong","label":"Strong shortlist","summary":"Good trust signals with a few areas worth checking before rollout.","recommendedAction":"Test in a sandbox workflow and compare its install path with close alternatives.","dimensions":[{"id":"github_adoption","label":"GitHub adoption","score":100,"weight":0.13,"status":"pass","detail":"38K GitHub stars"},{"id":"repo_activity","label":"Stars/forks activity","score":97,"weight":0.08,"status":"pass","detail":"38K stars, 3.6K forks; issue activity unavailable in current metadata"},{"id":"maintenance","label":"Recent maintenance","score":100,"weight":0.14,"status":"pass","detail":"6d since push"},{"id":"license","label":"License clarity","score":86,"weight":0.09,"status":"pass","detail":"https://creativecommons.org/licenses/by/4.0/"},{"id":"documentation","label":"README/SKILL.md completeness","score":86,"weight":0.14,"status":"pass","detail":"Metadata includes enough usage and workflow context"},{"id":"dependency_risk","label":"Dependency/runtime risk","score":54,"weight":0.12,"status":"warn","detail":"command execution surface, external package install surface"},{"id":"installability","label":"Install availability","score":92,"weight":0.1,"status":"pass","detail":"npx skills add K-Dense-AI/scientific-agent-skills --skill bids"},{"id":"install_safety","label":"Install command safety","score":92,"weight":0.1,"status":"pass","detail":"standard package or runtime install path"},{"id":"permission_surface","label":"Permission surface","score":50,"weight":0.07,"status":"warn","detail":"shell or command execution, filesystem or document access"},{"id":"repository","label":"Repository evidence","score":86,"weight":0.04,"status":"pass","detail":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/bids"},{"id":"review_status","label":"Review status","score":66,"weight":0.05,"status":"info","detail":"AI review data available"},{"id":"agent_outcomes","label":"Agent Proven outcomes","score":54,"weight":0.13,"status":"info","detail":"No agent outcome data yet"}],"checks":[{"status":"pass","label":"GitHub adoption","detail":"38K GitHub stars"},{"status":"pass","label":"Stars/forks activity","detail":"38K stars, 3.6K forks; issue activity unavailable in current metadata"},{"status":"pass","label":"Recent maintenance","detail":"6d since push"},{"status":"pass","label":"License clarity","detail":"https://creativecommons.org/licenses/by/4.0/"},{"status":"pass","label":"README/SKILL.md completeness","detail":"Metadata includes enough usage and workflow context"},{"status":"warn","label":"Dependency/runtime risk","detail":"command execution surface, external package install surface"},{"status":"pass","label":"Install availability","detail":"npx skills add K-Dense-AI/scientific-agent-skills --skill bids"},{"status":"pass","label":"Install command safety","detail":"standard package or runtime install path"},{"status":"warn","label":"Permission surface","detail":"shell or command execution, filesystem or document access"},{"status":"pass","label":"Repository evidence","detail":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/bids"},{"status":"info","label":"Review status","detail":"AI review data available"},{"status":"info","label":"Agent Proven outcomes","detail":"No agent outcome data yet"},{"status":"warn","label":"Ownership","detail":"No approved owner claim yet"},{"status":"pass","label":"OpenAgentSkill usage","detail":"5 views, 0 install copies"},{"status":"info","label":"Agent outcomes","detail":"No agent outcome data yet"}],"strengths":["AI review approved","Install path is available","Repository evidence is available","Recently maintained repository","Large GitHub adoption signal","Install command has no obvious high-risk pattern"],"warnings":["The alternative Deno install command uses `-A` (allow all permissions), which grants excessive permissions to a globally installed script; this should be scoped or clearly explained if the agent is expected to run it.","Permission surface needs review: shell or command execution, filesystem or document access","Dependency/runtime risk: command execution surface, external package install surface","Permission surface: shell or command execution, filesystem or document access"],"evidence":{"stars":"38K GitHub stars","repoActivity":"38K stars, 3.6K forks","lastPushed":"6d since push","license":"https://creativecommons.org/licenses/by/4.0/","repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/bids","install":"npx skills add K-Dense-AI/scientific-agent-skills --skill bids","installSafety":"standard package or runtime install path","permissionSurface":"shell or command execution, filesystem or document access","documentation":"Strong README/SKILL.md context","agentOutcomes":"No agent outcome data yet"},"installReadiness":{"ready":true,"command":"npx skills add K-Dense-AI/scientific-agent-skills --skill bids","policy":"human_review_before_install","label":"Human review before install","notes":["Install path is available","Repository evidence is available","License is declared","No Agent Proven outcome evidence yet","6d since push"]},"agentCompatibility":["Codex","Claude Code","Cursor","OpenAgentSkill CLI"],"riskSummary":{"level":"medium","label":"Review before production","notes":["The alternative Deno install command uses `-A` (allow all permissions), which grants excessive permissions to a globally installed script; this should be scoped or clearly explained if the agent is expected to run it.","Permission surface needs review: shell or command execution, filesystem or document access","Dependency/runtime risk: command execution surface, external package install surface","Permission surface: shell or command execution, filesystem or document access"]},"outcomeEvidence":{"total":0,"successes":0,"failures":0,"notRelevant":0,"successRate":null,"installAttempts":0,"riskBlocked":0,"setupRequired":0,"installSuccessRate":null,"avgOutputQuality":null,"avgTimeToUsefulMs":null,"productionOutcomes":0,"humanReviewRequired":0,"recentSuccessRate":null,"recentFailureRate":null,"uniqueAgents":0,"agentProvenScore":0,"agentProvenLabel":"Needs first agent run","lastOutcomeAt":null,"label":"No agent outcome data yet"},"autoInstall":{"allowed":false,"sandboxRequired":true,"policy":"human_review_before_install","reason":"Human review or sandbox validation is required before automatic installation."},"bestFor":["security","agent-skill"],"doNotUseFor":["Production credentials, payments, or irreversible account changes without explicit human review","Sensitive private data before reviewing repository code, license, and permission surface","Automatic installation in a production workspace"],"knownRisks":["The alternative Deno install command uses `-A` (allow all permissions), which grants excessive permissions to a globally installed script; this should be scoped or clearly explained if the agent is expected to run it.","Permission surface needs review: shell or command execution, filesystem or document access","Dependency/runtime risk: command execution surface, external package install surface","Permission surface: shell or command execution, filesystem or document access"]},"agent_proven":{"version":"agent-proven-v1","score":0,"tier":"unproven","label":"Needs first agent run","summary":"No agent outcome reports yet. Use Resolve, run one narrow sandbox task, then report the result.","metrics":{"totalOutcomes":0,"successfulOutcomes":0,"failedOutcomes":0,"installAttempts":0,"installSuccessRate":null,"successRate":null,"recentSuccessRate":null,"recentFailureRate":null,"riskBlocked":0,"setupRequired":0,"notRelevant":0,"avgOutputQuality":null,"avgTimeToUsefulMs":null,"productionOutcomes":0,"humanReviewRequired":0,"uniqueAgents":0,"lastOutcomeAt":null},"signals":[],"penalties":["No real agent outcome evidence yet"]},"outcome_stats":null,"safety":{"score":53,"level":"avoid_auto_install","label":"Avoid automatic install","safety_tier":{"tier":"experimental","label":"Experimental","badge":"EXPERIMENTAL","summary":"Sparse or mixed signals. Useful for discovery, but not for autonomous installation.","recommended_action":"Test manually in an isolated workspace and compare against safer alternatives.","auto_install_policy":"review","reasons":["High-risk permission hints: Shell or command execution","53/100 agent safety score"]},"auto_install_allowed":false,"human_review_required":true,"blocked":false,"audit_risk":"needs_review","permission_hints":[{"id":"shell","label":"Shell or command execution","reason":"Skill metadata references terminal, CLI, shell, subprocess, or command execution workflows.","severity":"high"},{"id":"network","label":"Network access","reason":"Skill likely fetches remote pages, APIs, repositories, or external services.","severity":"medium"},{"id":"filesystem","label":"Filesystem access","reason":"Skill may read or write project files, documents, generated artifacts, or local workspace state.","severity":"medium"},{"id":"database","label":"Database access","reason":"Skill may inspect schemas, query databases, or work with persistent stores.","severity":"medium"}],"policy_warnings":["High-risk permission hints: Shell or command execution","Dependency or permission surface needs review"],"constraints_applied":{"max_risk":"medium","needs_install_command":true,"min_stars":0}},"safety_gate":{"tier":"experimental","label":"Experimental","badge":"EXPERIMENTAL","auto_install_policy":"review","auto_install_allowed":false,"blocked":false,"human_review_required":true,"recommended_action":"Test manually in an isolated workspace and compare against safer alternatives.","reasons":["High-risk permission hints: Shell or command execution","53/100 agent safety score"]},"eval":{"version":"openagentskill-skill-eval-v1","status":"failed","score":77,"risk_level":"high","decision":{"recommendation":"do_not_auto_install","reason":"Permission surface: shell or command execution, filesystem or document access","auto_install_allowed":false,"policy":"block","human_review_required":true},"blockers":["Permission surface: shell or command execution, filesystem or document access"],"warnings":["Trust score: Good trust signals with a few areas worth checking before rollout.","Audit score: Needs review","Agent safety gate: Sparse or mixed signals. Useful for discovery, but not for autonomous installation.","High-risk permission hints: Shell or command execution","Dependency or permission surface needs review","Permission surface may require sandboxing","The alternative Deno install command uses `-A` (allow all permissions), which grants excessive permissions to a globally installed script; this should be scoped or clearly explained if the agent is expected to run it.","SKILL.md describes when to use the skill but lacks an explicit \"When not to use\" / limitations section, such as BIDS specification version drift, the need to manually verify DICOM conversion heuristics, and validation before dataset sharing.","Permission surface needs review: shell or command execution, filesystem or document access","Dependency/runtime risk: command execution surface, external package install surface","Permission surface: shell or command execution, filesystem or document access"],"validation_plan":["Inspect repository, README/SKILL.md, license, and recent commits before production use.","Install in an isolated workspace or sandbox with no production secrets available.","Run the smallest representative task and record files touched, commands run, network access, and outputs.","Compare the selected skill against at least one alternative when the eval status is review or failed.","Promote only after the agent reports a successful verification result and unresolved warnings are accepted."],"checks":[{"id":"task_fit","label":"Task fit","status":"pass","score":84,"required_for_auto_install":true,"detail":"Task wording matches this skill metadata.","evidence":["Evaluate bids before installing it in an agent workflow","security","GitHub automation workflows; Claude Code teams; teams that value GitHub adoption signals"]},{"id":"install_path","label":"Install path","status":"pass","score":92,"required_for_auto_install":true,"detail":"Install handoff is available.","evidence":["npx skills add K-Dense-AI/scientific-agent-skills --skill bids"]},{"id":"install_safety","label":"Install command safety","status":"pass","score":92,"required_for_auto_install":true,"detail":"standard package or runtime install path","evidence":["npx skills add K-Dense-AI/scientific-agent-skills --skill bids"]},{"id":"trust_score","label":"Trust score","status":"warn","score":75,"required_for_auto_install":true,"detail":"Good trust signals with a few areas worth checking before rollout.","evidence":["Strong shortlist","38K GitHub stars","https://creativecommons.org/licenses/by/4.0/"]},{"id":"audit_score","label":"Audit score","status":"warn","score":85,"required_for_auto_install":true,"detail":"Needs review","evidence":["Dependency or permission surface needs review"]},{"id":"agent_safety_gate","label":"Agent safety gate","status":"warn","score":53,"required_for_auto_install":true,"detail":"Sparse or mixed signals. Useful for discovery, but not for autonomous installation.","evidence":["Test manually in an isolated workspace and compare against safer alternatives.","High-risk permission hints: Shell or command execution"]},{"id":"readme_skillmd_completeness","label":"README/SKILL.md completeness","status":"pass","score":86,"required_for_auto_install":false,"detail":"Metadata includes enough usage and workflow context","evidence":["Strong README/SKILL.md context"]},{"id":"license_clarity","label":"License clarity","status":"pass","score":86,"required_for_auto_install":true,"detail":"https://creativecommons.org/licenses/by/4.0/","evidence":["https://creativecommons.org/licenses/by/4.0/"]},{"id":"recent_maintenance","label":"Recent maintenance","status":"pass","score":100,"required_for_auto_install":false,"detail":"6d since push","evidence":["6d since push"]},{"id":"permission_surface","label":"Permission surface","status":"fail","score":50,"required_for_auto_install":true,"detail":"shell or command execution, filesystem or document access","evidence":["Shell or command execution: high","Network access: medium","Filesystem access: medium"]},{"id":"alternatives","label":"Alternatives available","status":"info","score":55,"required_for_auto_install":false,"detail":"No close alternatives were found in the current shortlist.","evidence":[]}],"endpoints":{"web":"https://www.openagentskill.com/skills/k-dense-ai-bids/evals","api":"/api/agent/evals?slug=k-dense-ai-bids","text":"/api/agent/evals?slug=k-dense-ai-bids&format=text"}},"agent_readable_metadata":{"version":"openagentskill-agent-metadata-v2","skill":{"slug":"k-dense-ai-bids","name":"bids","description":"Use this skill when working with Brain Imaging Data Structure (BIDS) datasets: organizing neuroscience and biomedical data (MRI, EEG, MEG, iEEG, PET, microscopy, NIRS, motion capture, EMG, MR spectroscopy, behavioral), querying BIDS layouts, validating compliance, converting DICOM to BIDS, writing metadata sidecars, or creating BIDS derivatives.","category":"security","url":"https://www.openagentskill.com/skills/k-dense-ai-bids","repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/bids","github_repo":"K-Dense-AI/scientific-agent-skills"},"suited_tasks":["GitHub automation workflows","Claude Code teams","teams that value GitHub adoption signals","Inspect repository metadata","Compare code changes","Write concise engineering summaries","Search sources","Extract claims"],"suited_agents":["Codex","Claude Code","Cursor","OpenAgentSkill CLI","CLI"],"install":{"command":"npx skills add K-Dense-AI/scientific-agent-skills --skill bids","ready":true,"targets":[{"id":"openagentskill-cli","label":"CLI","kind":"command","value":"npx --yes https://github.com/Leon-Drq/openagentskill/releases/download/cli-v0.3.0/openagentskill-0.3.0.tgz add k-dense-ai-bids"},{"id":"codex","label":"Codex","kind":"agent-prompt","value":"Install the \"bids\" agent skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/bids. Read its SKILL.md or equivalent instructions first, install only the files needed for this workspace, and summarize any required setup before using it. Skill purpose: Use this skill when working with Brain Imaging Data Structure (BIDS) datasets: organizing neuroscience and biomedical data (MRI, EEG, MEG, iEEG, PET, microscopy, NIRS, motion capture, EMG, MR spectroscopy, behavioral), querying BIDS layouts, validating compliance, converting DICOM to BIDS, writing metadata sidecars, or creating BIDS derivatives. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"k-dense-ai-bids\",\"task\":\"Install bids\",\"agent\":\"codex\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes."},{"id":"claude-code","label":"Claude Code","kind":"agent-prompt","value":"Add \"bids\" as a Claude Code skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/bids. Inspect the skill instructions, place the reusable skill files in the appropriate local skills location for this project, and report the activation steps. Skill purpose: Use this skill when working with Brain Imaging Data Structure (BIDS) datasets: organizing neuroscience and biomedical data (MRI, EEG, MEG, iEEG, PET, microscopy, NIRS, motion capture, EMG, MR spectroscopy, behavioral), querying BIDS layouts, validating compliance, converting DICOM to BIDS, writing metadata sidecars, or creating BIDS derivatives. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"k-dense-ai-bids\",\"task\":\"Install bids\",\"agent\":\"claude-code\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes."},{"id":"cursor","label":"Cursor","kind":"agent-prompt","value":"Turn \"bids\" from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/bids into a reusable Cursor project rule or agent instruction. Preserve the core workflow, adapt paths to this repo, and keep the rule scoped to tasks where it is relevant. Skill purpose: Use this skill when working with Brain Imaging Data Structure (BIDS) datasets: organizing neuroscience and biomedical data (MRI, EEG, MEG, iEEG, PET, microscopy, NIRS, motion capture, EMG, MR spectroscopy, behavioral), querying BIDS layouts, validating compliance, converting DICOM to BIDS, writing metadata sidecars, or creating BIDS derivatives. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"k-dense-ai-bids\",\"task\":\"Install bids\",\"agent\":\"cursor\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes."}],"handoff_url":"https://www.openagentskill.com/api/skills/k-dense-ai-bids/install","manifest_url":"https://www.openagentskill.com/api/registry/manifest/k-dense-ai-bids"},"trust":{"score":75,"label":"Strong shortlist","version":"trust-score-v4","install_policy":"human_review_before_install","evidence":{"stars":"38K GitHub stars","repoActivity":"38K stars, 3.6K forks","lastPushed":"6d since push","license":"https://creativecommons.org/licenses/by/4.0/","repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/bids","install":"npx skills add K-Dense-AI/scientific-agent-skills --skill bids","installSafety":"standard package or runtime install path","permissionSurface":"shell or command execution, filesystem or document access","documentation":"Strong README/SKILL.md context","agentOutcomes":"No agent outcome data yet"},"outcome_evidence":{"total":0,"successes":0,"failures":0,"not_relevant":0,"success_rate":null,"recent_success_rate":null,"recent_failure_rate":null,"install_attempts":0,"install_success_rate":null,"risk_blocked":0,"setup_required":0,"avg_output_quality":null,"production_outcomes":0,"last_outcome_at":null,"label":"No agent outcome data yet"},"auto_install":{"allowed":false,"sandbox_required":true,"reason":"Human review or sandbox validation is required before automatic installation."},"best_for":["security","agent-skill"],"known_risks":["The alternative Deno install command uses `-A` (allow all permissions), which grants excessive permissions to a globally installed script; this should be scoped or clearly explained if the agent is expected to run it.","Permission surface needs review: shell or command execution, filesystem or document access","Dependency/runtime risk: command execution surface, external package install surface","Permission surface: shell or command execution, filesystem or document access"]},"agent_proven":{"version":"agent-proven-v1","score":0,"tier":"unproven","label":"Needs first agent run","summary":"No agent outcome reports yet. Use Resolve, run one narrow sandbox task, then report the result.","metrics":{"totalOutcomes":0,"successfulOutcomes":0,"failedOutcomes":0,"installAttempts":0,"installSuccessRate":null,"successRate":null,"recentSuccessRate":null,"recentFailureRate":null,"riskBlocked":0,"setupRequired":0,"notRelevant":0,"avgOutputQuality":null,"avgTimeToUsefulMs":null,"productionOutcomes":0,"humanReviewRequired":0,"uniqueAgents":0,"lastOutcomeAt":null},"signals":[],"penalties":["No real agent outcome evidence yet"]},"audit":{"score":85,"risk_level":"needs_review","risk_label":"Needs review","warnings":["Dependency or permission surface needs review","Permission surface may require sandboxing","The alternative Deno install command uses `-A` (allow all permissions), which grants excessive permissions to a globally installed script; this should be scoped or clearly explained if the agent is expected to run it.","SKILL.md describes when to use the skill but lacks an explicit \"When not to use\" / limitations section, such as BIDS specification version drift, the need to manually verify DICOM conversion heuristics, and validation before dataset sharing.","Permission surface needs review: shell or command execution, filesystem or document access","Dependency/runtime risk: command execution surface, external package install surface","Permission surface: shell or command execution, filesystem or document access"]},"safety_gate":{"tier":"experimental","label":"Experimental","auto_install_policy":"review","auto_install_allowed":false,"human_review_required":true,"blocked":false,"recommended_action":"Test manually in an isolated workspace and compare against safer alternatives."},"quality":{"score":92,"label":"Excellent"},"supply":{"track":"Coding and developer agents","scenario":"GitHub automation","maintenance":"6d since push","risk":"Needs review"},"alternative_skills":[],"do_not_use_when":["teams that need a vendor-supported SLA","production agents without a repository review","The alternative Deno install command uses `-A` (allow all permissions), which grants excessive permissions to a globally installed script; this should be scoped or clearly explained if the agent is expected to run it.","High-risk permission hints: Shell or command execution","Dependency or permission surface needs review","Permission surface may require sandboxing","SKILL.md describes when to use the skill but lacks an explicit \"When not to use\" / limitations section, such as BIDS specification version drift, the need to manually verify DICOM conversion heuristics, and validation before dataset sharing.","Permission surface needs review: shell or command execution, filesystem or document access"],"agent_contract":{"task_input":"Use bids in an agent workflow","recommended_action":"Test manually in an isolated workspace and compare against safer alternatives.","install_policy":"review","minimum_review_before_use":["Trust: 75/100 Strong shortlist","Audit: 85/100 Needs review","Safety: 53/100 Avoid automatic install","Review repository, license, install command, and permission surface before production use."],"expected_agent_output":{"selected_skill":"k-dense-ai-bids (bids)","install_command":"npx skills add K-Dense-AI/scientific-agent-skills --skill bids","risk_summary":"Needs review; Experimental; Review before production","verification_result":"Report the smallest successful task, files touched, warnings, and any missing setup."}},"outcome_feedback":{"endpoint":"https://www.openagentskill.com/api/agent/outcome","method":"POST","requires_resolve_event_id":true,"event_id_source":"Use install_receipt.outcome_feedback.event_id or feedback.event_id returned by /api/agent/resolve for the current task.","expected_outcomes":["success","failed","not_relevant","blocked_by_risk","setup_required"],"payload_template":{"event_id":"<install_receipt.outcome_feedback.event_id or feedback.event_id from /api/agent/resolve>","skill_slug":"k-dense-ai-bids","task":"Use bids in an agent workflow","agent":"codex","outcome":"success","install_used":true,"risk_blocked":false,"setup_required":false,"task_success":true,"output_quality":4,"error_type":null,"human_review_required":false,"workspace":"sandbox","time_to_useful_ms":120000,"notes":"Report the smallest successful task, setup friction, files touched, and risk notes."}},"endpoints":{"web":"https://www.openagentskill.com/skills/k-dense-ai-bids","api":"https://www.openagentskill.com/api/agent/skills/k-dense-ai-bids","audit":"https://www.openagentskill.com/skills/k-dense-ai-bids/audit","eval":"https://www.openagentskill.com/api/agent/evals?slug=k-dense-ai-bids&task=Use%20bids%20in%20an%20agent%20workflow&max_risk=medium","resolve":"https://www.openagentskill.com/api/agent/resolve?task=Use%20bids%20in%20an%20agent%20workflow&agent=codex&max_risk=medium","receipt":"https://www.openagentskill.com/api/agent/receipt?task=Use%20bids%20in%20an%20agent%20workflow&agent=codex&max_risk=medium&format=text","install":"https://www.openagentskill.com/api/skills/k-dense-ai-bids/install","manifest":"https://www.openagentskill.com/api/registry/manifest/k-dense-ai-bids"}},"machine_metadata":{"version":"openagentskill-agent-metadata-v2","skill":{"slug":"k-dense-ai-bids","name":"bids","description":"Use this skill when working with Brain Imaging Data Structure (BIDS) datasets: organizing neuroscience and biomedical data (MRI, EEG, MEG, iEEG, PET, microscopy, NIRS, motion capture, EMG, MR spectroscopy, behavioral), querying BIDS layouts, validating compliance, converting DICOM to BIDS, writing metadata sidecars, or creating BIDS derivatives.","category":"security","url":"https://www.openagentskill.com/skills/k-dense-ai-bids","repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/bids","github_repo":"K-Dense-AI/scientific-agent-skills"},"suited_tasks":["GitHub automation workflows","Claude Code teams","teams that value GitHub adoption signals","Inspect repository metadata","Compare code changes","Write concise engineering summaries","Search sources","Extract claims"],"suited_agents":["Codex","Claude Code","Cursor","OpenAgentSkill CLI","CLI"],"install":{"command":"npx skills add K-Dense-AI/scientific-agent-skills --skill bids","ready":true,"targets":[{"id":"openagentskill-cli","label":"CLI","kind":"command","value":"npx --yes https://github.com/Leon-Drq/openagentskill/releases/download/cli-v0.3.0/openagentskill-0.3.0.tgz add k-dense-ai-bids"},{"id":"codex","label":"Codex","kind":"agent-prompt","value":"Install the \"bids\" agent skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/bids. Read its SKILL.md or equivalent instructions first, install only the files needed for this workspace, and summarize any required setup before using it. Skill purpose: Use this skill when working with Brain Imaging Data Structure (BIDS) datasets: organizing neuroscience and biomedical data (MRI, EEG, MEG, iEEG, PET, microscopy, NIRS, motion capture, EMG, MR spectroscopy, behavioral), querying BIDS layouts, validating compliance, converting DICOM to BIDS, writing metadata sidecars, or creating BIDS derivatives. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"k-dense-ai-bids\",\"task\":\"Install bids\",\"agent\":\"codex\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes."},{"id":"claude-code","label":"Claude Code","kind":"agent-prompt","value":"Add \"bids\" as a Claude Code skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/bids. Inspect the skill instructions, place the reusable skill files in the appropriate local skills location for this project, and report the activation steps. Skill purpose: Use this skill when working with Brain Imaging Data Structure (BIDS) datasets: organizing neuroscience and biomedical data (MRI, EEG, MEG, iEEG, PET, microscopy, NIRS, motion capture, EMG, MR spectroscopy, behavioral), querying BIDS layouts, validating compliance, converting DICOM to BIDS, writing metadata sidecars, or creating BIDS derivatives. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"k-dense-ai-bids\",\"task\":\"Install bids\",\"agent\":\"claude-code\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes."},{"id":"cursor","label":"Cursor","kind":"agent-prompt","value":"Turn \"bids\" from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/bids into a reusable Cursor project rule or agent instruction. Preserve the core workflow, adapt paths to this repo, and keep the rule scoped to tasks where it is relevant. Skill purpose: Use this skill when working with Brain Imaging Data Structure (BIDS) datasets: organizing neuroscience and biomedical data (MRI, EEG, MEG, iEEG, PET, microscopy, NIRS, motion capture, EMG, MR spectroscopy, behavioral), querying BIDS layouts, validating compliance, converting DICOM to BIDS, writing metadata sidecars, or creating BIDS derivatives. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"k-dense-ai-bids\",\"task\":\"Install bids\",\"agent\":\"cursor\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes."}],"handoff_url":"https://www.openagentskill.com/api/skills/k-dense-ai-bids/install","manifest_url":"https://www.openagentskill.com/api/registry/manifest/k-dense-ai-bids"},"trust":{"score":75,"label":"Strong shortlist","version":"trust-score-v4","install_policy":"human_review_before_install","evidence":{"stars":"38K GitHub stars","repoActivity":"38K stars, 3.6K forks","lastPushed":"6d since push","license":"https://creativecommons.org/licenses/by/4.0/","repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/bids","install":"npx skills add K-Dense-AI/scientific-agent-skills --skill bids","installSafety":"standard package or runtime install path","permissionSurface":"shell or command execution, filesystem or document access","documentation":"Strong README/SKILL.md context","agentOutcomes":"No agent outcome data yet"},"outcome_evidence":{"total":0,"successes":0,"failures":0,"not_relevant":0,"success_rate":null,"recent_success_rate":null,"recent_failure_rate":null,"install_attempts":0,"install_success_rate":null,"risk_blocked":0,"setup_required":0,"avg_output_quality":null,"production_outcomes":0,"last_outcome_at":null,"label":"No agent outcome data yet"},"auto_install":{"allowed":false,"sandbox_required":true,"reason":"Human review or sandbox validation is required before automatic installation."},"best_for":["security","agent-skill"],"known_risks":["The alternative Deno install command uses `-A` (allow all permissions), which grants excessive permissions to a globally installed script; this should be scoped or clearly explained if the agent is expected to run it.","Permission surface needs review: shell or command execution, filesystem or document access","Dependency/runtime risk: command execution surface, external package install surface","Permission surface: shell or command execution, filesystem or document access"]},"agent_proven":{"version":"agent-proven-v1","score":0,"tier":"unproven","label":"Needs first agent run","summary":"No agent outcome reports yet. Use Resolve, run one narrow sandbox task, then report the result.","metrics":{"totalOutcomes":0,"successfulOutcomes":0,"failedOutcomes":0,"installAttempts":0,"installSuccessRate":null,"successRate":null,"recentSuccessRate":null,"recentFailureRate":null,"riskBlocked":0,"setupRequired":0,"notRelevant":0,"avgOutputQuality":null,"avgTimeToUsefulMs":null,"productionOutcomes":0,"humanReviewRequired":0,"uniqueAgents":0,"lastOutcomeAt":null},"signals":[],"penalties":["No real agent outcome evidence yet"]},"audit":{"score":85,"risk_level":"needs_review","risk_label":"Needs review","warnings":["Dependency or permission surface needs review","Permission surface may require sandboxing","The alternative Deno install command uses `-A` (allow all permissions), which grants excessive permissions to a globally installed script; this should be scoped or clearly explained if the agent is expected to run it.","SKILL.md describes when to use the skill but lacks an explicit \"When not to use\" / limitations section, such as BIDS specification version drift, the need to manually verify DICOM conversion heuristics, and validation before dataset sharing.","Permission surface needs review: shell or command execution, filesystem or document access","Dependency/runtime risk: command execution surface, external package install surface","Permission surface: shell or command execution, filesystem or document access"]},"safety_gate":{"tier":"experimental","label":"Experimental","auto_install_policy":"review","auto_install_allowed":false,"human_review_required":true,"blocked":false,"recommended_action":"Test manually in an isolated workspace and compare against safer alternatives."},"quality":{"score":92,"label":"Excellent"},"supply":{"track":"Coding and developer agents","scenario":"GitHub automation","maintenance":"6d since push","risk":"Needs review"},"alternative_skills":[],"do_not_use_when":["teams that need a vendor-supported SLA","production agents without a repository review","The alternative Deno install command uses `-A` (allow all permissions), which grants excessive permissions to a globally installed script; this should be scoped or clearly explained if the agent is expected to run it.","High-risk permission hints: Shell or command execution","Dependency or permission surface needs review","Permission surface may require sandboxing","SKILL.md describes when to use the skill but lacks an explicit \"When not to use\" / limitations section, such as BIDS specification version drift, the need to manually verify DICOM conversion heuristics, and validation before dataset sharing.","Permission surface needs review: shell or command execution, filesystem or document access"],"agent_contract":{"task_input":"Use bids in an agent workflow","recommended_action":"Test manually in an isolated workspace and compare against safer alternatives.","install_policy":"review","minimum_review_before_use":["Trust: 75/100 Strong shortlist","Audit: 85/100 Needs review","Safety: 53/100 Avoid automatic install","Review repository, license, install command, and permission surface before production use."],"expected_agent_output":{"selected_skill":"k-dense-ai-bids (bids)","install_command":"npx skills add K-Dense-AI/scientific-agent-skills --skill bids","risk_summary":"Needs review; Experimental; Review before production","verification_result":"Report the smallest successful task, files touched, warnings, and any missing setup."}},"outcome_feedback":{"endpoint":"https://www.openagentskill.com/api/agent/outcome","method":"POST","requires_resolve_event_id":true,"event_id_source":"Use install_receipt.outcome_feedback.event_id or feedback.event_id returned by /api/agent/resolve for the current task.","expected_outcomes":["success","failed","not_relevant","blocked_by_risk","setup_required"],"payload_template":{"event_id":"<install_receipt.outcome_feedback.event_id or feedback.event_id from /api/agent/resolve>","skill_slug":"k-dense-ai-bids","task":"Use bids in an agent workflow","agent":"codex","outcome":"success","install_used":true,"risk_blocked":false,"setup_required":false,"task_success":true,"output_quality":4,"error_type":null,"human_review_required":false,"workspace":"sandbox","time_to_useful_ms":120000,"notes":"Report the smallest successful task, setup friction, files touched, and risk notes."}},"endpoints":{"web":"https://www.openagentskill.com/skills/k-dense-ai-bids","api":"https://www.openagentskill.com/api/agent/skills/k-dense-ai-bids","audit":"https://www.openagentskill.com/skills/k-dense-ai-bids/audit","eval":"https://www.openagentskill.com/api/agent/evals?slug=k-dense-ai-bids&task=Use%20bids%20in%20an%20agent%20workflow&max_risk=medium","resolve":"https://www.openagentskill.com/api/agent/resolve?task=Use%20bids%20in%20an%20agent%20workflow&agent=codex&max_risk=medium","receipt":"https://www.openagentskill.com/api/agent/receipt?task=Use%20bids%20in%20an%20agent%20workflow&agent=codex&max_risk=medium&format=text","install":"https://www.openagentskill.com/api/skills/k-dense-ai-bids/install","manifest":"https://www.openagentskill.com/api/registry/manifest/k-dense-ai-bids"}},"supply_profile":{"track":{"slug":"coding","label":"Coding and developer agents","shortLabel":"Coding","description":"Code review, repo analysis, testing, CI, GitHub, DevOps, and developer workflow skills."},"scenario":{"label":"GitHub automation","description":"I need my agent to triage GitHub issues, review pull requests, and summarize repository changes.","useCases":[{"slug":"github-automation","title":"GitHub automation"},{"slug":"research-agents","title":"Research agents"},{"slug":"coding-agents","title":"Coding agents"}]},"applicableAgents":["Claude Code","CLI","Codex","Cursor"],"install":{"ready":true,"command":"npx skills add K-Dense-AI/scientific-agent-skills --skill bids","primaryTarget":"CLI","targetCount":4},"githubQuality":{"stars":38487,"starsLabel":"38K","forks":3607,"license":"https://creativecommons.org/licenses/by/4.0/","qualityScore":92,"trustScore":75,"auditScore":85},"maintenance":{"status":"fresh","label":"6d since push","daysSincePush":6,"lastPushedAt":"2026-08-30T13:19:27+00:00"},"risk":{"level":"needs_review","label":"Needs review","requiresReview":true,"notes":["Dependency or permission surface needs review","Permission surface may require sandboxing","The alternative Deno install command uses `-A` (allow all permissions), which grants excessive permissions to a globally installed script; this should be scoped or clearly explained if the agent is expected to run it.","SKILL.md describes when to use the skill but lacks an explicit \"When not to use\" / limitations section, such as BIDS specification version drift, the need to manually verify DICOM conversion heuristics, and validation before dataset sharing.","Permission surface needs review: shell or command execution, filesystem or document access"]},"coverageTags":["Coding","GitHub automation","security","agent-skill"]},"audit":{"audit_score":85,"risk_level":"needs_review","risk_label":"Needs review","quality_score":92,"trust_score":75,"maintenance_score":100,"security_score":75,"install_score":92,"warnings":["Dependency or permission surface needs review","Permission surface may require sandboxing","The alternative Deno install command uses `-A` (allow all permissions), which grants excessive permissions to a globally installed script; this should be scoped or clearly explained if the agent is expected to run it.","SKILL.md describes when to use the skill but lacks an explicit \"When not to use\" / limitations section, such as BIDS specification version drift, the need to manually verify DICOM conversion heuristics, and validation before dataset sharing.","Permission surface needs review: shell or command execution, filesystem or document access","Dependency/runtime risk: command execution surface, external package install surface","Permission surface: shell or command execution, filesystem or document access"]},"quality_signals":{"model":"v2","star_score":32.1,"usage_score":0,"review_score":5.25,"metadata_score":3,"freshness_score":15},"platforms":["Claude Code"],"use_cases":[{"slug":"github-automation","title":"GitHub automation","url":"https://www.openagentskill.com/use-cases/github-automation"},{"slug":"research-agents","title":"Research agents","url":"https://www.openagentskill.com/use-cases/research-agents"},{"slug":"coding-agents","title":"Coding agents","url":"https://www.openagentskill.com/use-cases/coding-agents"},{"slug":"database-sql","title":"Database and SQL","url":"https://www.openagentskill.com/use-cases/database-sql"}],"stacks":[{"slug":"research-report-agent","title":"Research report agent","url":"https://www.openagentskill.com/collections/research-report-agent"},{"slug":"coding-review-agent","title":"Coding review agent","url":"https://www.openagentskill.com/collections/coding-review-agent"},{"slug":"content-growth-agent","title":"Content growth agent","url":"https://www.openagentskill.com/collections/content-growth-agent"}],"install":"npx skills add K-Dense-AI/scientific-agent-skills --skill bids","install_targets":[{"id":"openagentskill-cli","label":"CLI","title":"OpenAgentSkill CLI","kind":"command","value":"npx --yes https://github.com/Leon-Drq/openagentskill/releases/download/cli-v0.3.0/openagentskill-0.3.0.tgz add k-dense-ai-bids","description":"Resolve policy, run the source installer safely, and report a verified install receipt.","copyLabel":"Copy command"},{"id":"codex","label":"Codex","title":"Codex install prompt","kind":"agent-prompt","value":"Install the \"bids\" agent skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/bids. Read its SKILL.md or equivalent instructions first, install only the files needed for this workspace, and summarize any required setup before using it. Skill purpose: Use this skill when working with Brain Imaging Data Structure (BIDS) datasets: organizing neuroscience and biomedical data (MRI, EEG, MEG, iEEG, PET, microscopy, NIRS, motion capture, EMG, MR spectroscopy, behavioral), querying BIDS layouts, validating compliance, converting DICOM to BIDS, writing metadata sidecars, or creating BIDS derivatives. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"k-dense-ai-bids\",\"task\":\"Install bids\",\"agent\":\"codex\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes.","description":"Give Codex a repo-aware install prompt when the skill is not available through a local CLI.","copyLabel":"Copy prompt"},{"id":"claude-code","label":"Claude Code","title":"Claude Code skill prompt","kind":"agent-prompt","value":"Add \"bids\" as a Claude Code skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/bids. Inspect the skill instructions, place the reusable skill files in the appropriate local skills location for this project, and report the activation steps. Skill purpose: Use this skill when working with Brain Imaging Data Structure (BIDS) datasets: organizing neuroscience and biomedical data (MRI, EEG, MEG, iEEG, PET, microscopy, NIRS, motion capture, EMG, MR spectroscopy, behavioral), querying BIDS layouts, validating compliance, converting DICOM to BIDS, writing metadata sidecars, or creating BIDS derivatives. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"k-dense-ai-bids\",\"task\":\"Install bids\",\"agent\":\"claude-code\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes.","description":"Use this prompt to ask Claude Code to add the skill and explain the local activation steps.","copyLabel":"Copy prompt"},{"id":"cursor","label":"Cursor","title":"Cursor rule prompt","kind":"agent-prompt","value":"Turn \"bids\" from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/bids into a reusable Cursor project rule or agent instruction. Preserve the core workflow, adapt paths to this repo, and keep the rule scoped to tasks where it is relevant. Skill purpose: Use this skill when working with Brain Imaging Data Structure (BIDS) datasets: organizing neuroscience and biomedical data (MRI, EEG, MEG, iEEG, PET, microscopy, NIRS, motion capture, EMG, MR spectroscopy, behavioral), querying BIDS layouts, validating compliance, converting DICOM to BIDS, writing metadata sidecars, or creating BIDS derivatives. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"k-dense-ai-bids\",\"task\":\"Install bids\",\"agent\":\"cursor\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes.","description":"Use this when installing as Cursor project rules or reusable agent instructions.","copyLabel":"Copy prompt"}],"repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/bids","github_repo":"K-Dense-AI/scientific-agent-skills","version":"1.0.0","license":"https://creativecommons.org/licenses/by/4.0/","urls":{"web":"https://www.openagentskill.com/skills/k-dense-ai-bids","repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/bids","api":"/api/agent/skills/k-dense-ai-bids","install_api":"/api/skills/k-dense-ai-bids/install"},"meta":{"created_at":"2026-08-30T13:22:24.775652+00:00","updated_at":"2026-09-01T11:59:28.941454+00:00","agent_friendly":true}}