bids-organizer
Use this skill whenever the user wants to automatically organize raw neuroimaging data (DICOM, NIfTI, EEG, etc.) into a valid BIDS (Brain Imaging Data Structure) dataset. Triggers include: 'organize to BIDS', 'BIDS organizer', 'convert to BIDS', 'BIDS conversion', 'bidsify', 'create BIDS dataset', 'raw data to BIDS', or any request to structure data according to BIDS specification.
npx skills add BioTender-max/awesome-bio-agent-skills --skill bids-organizer --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# BIDS Organizer (Tool Layer) ## Overview BIDS Organizer is the NeuroClaw interface-layer skill that automatically converts raw or semi-organized neuroimaging data into a standardized BIDS-compliant dataset. It supports DICOM → NIfTI conversion + BIDS naming, existing NIfTI reorganization, EEG (.set/.edf/.bdf/.fif), and basic metadata handling. The skill generates a clear execution plan, waits for user confirmation, then delegates all heavy work to appropriate base tools. **Core workflow (never bypassed):** 1. Scan input directory and detect data types (DICOM, NIfTI, EEG, etc.). 2. Generate a numbered execution plan with proposed BIDS structure and subject/session labels. 3. Present the plan, estimated time, and risks; wait for explicit confirmation (“YES” / “execute” / “proceed”). 4. On confirmation, delegate tasks to `dcm2nii`, `mne-eeg-tool`, and `claw-shell`. 5. After completion, run BIDS validation and generate a summary report. **Research use only.** ## Quick Reference | Task | What needs to be done | Delegate to which tool skill | Expected output | |-----------------------------------|------------------------------------------------------------|------------------------------
- Overview
- Quick Reference
- Common Shell Command Examples
- Installation (Handled by dependency-planner)
- NeuroClaw recommended wrapper script
- Important Notes & Limitations
- When to Call This Skill
- Benchmark-Facing Default Mainline
- Direct Mixed-Modality Benchmark Path
- Existing DWI NIfTI Sidecar Path
- Structural MRI Narrow Path
- Post-Execution Verification (Harness Integration)
- Complementary / Related Skills
- More Advanced Features
DICOM to BIDS (most common) dcm2niix -o ./bids/sub-001/ses-01/anat -f "%p_%s" -b y -z y /path/to/dicom/T1 Validate the resulting BIDS dataset bids-validator /path/to/bids_dataset dcm2niix --version bids-validator --version
What does the bids-organizer skill do?
Use this skill whenever the user wants to automatically organize raw neuroimaging data (DICOM, NIfTI, EEG, etc.) into a valid BIDS (Brain Imaging Data Structure) dataset. Triggers include: 'organize to BIDS', 'BIDS organizer', 'convert to BIDS', 'BIDS conversion', 'bidsify', 'create BIDS dataset', 'raw data to BIDS', or any request to structure data according to BIDS specification.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill bids-organizer --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.