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NeuroClaw Logo

NeuroClaw: Closed-Loop Agentic AI for Executable and Reproducible Neuroimaging Research

CUHK logo Β Β Β Β Β  Massachusetts General Hospital logo Β Β Β Β Β  Lehigh University logo

Python Platform License Skills arXiv Homepage NeuroOracle

δΈ­ζ–‡η‰ˆ README

Features β€’ Quick Start β€’ Project Structure β€’ Skills β€’ Acknowledgments

πŸ“– Overview

NeuroClaw is a research assistant for executable and reproducible neuroimaging research. Its core strength is neuroimaging dataset and model adaptation: turning raw scans into usable inputs quickly, and enabling medical practitioners to run deep learning models with minimal setup.

Neuroimaging datasets demand specialized preprocessing, and preprocessing quality directly determines model validity. Many workflows assume curated datasets, while MedicalClaw provides limited automation for open-source model execution (primarily large projects like TimesFM and AlphaFold), leaving users to spend significant time on environment configuration.

NeuroClaw prioritizes data processing and model configuration/execution. It ships with independent GUI and CLI interfaces for day-to-day use, and can also be installed as a reusable skill library inside agent projects such as OpenClaw, Hermes, and Claude Code.


πŸš€ Updates

  • [2026.06.20]: NeuroClaw now provides Windows and macOS desktop clients, while Linux remains supported through the repository and command-line/web workflows.
  • [2026.05.23]: NeuroBench now covers both data processing and model training/evaluation.
  • [2026.05.20]: 7 atoms Γ— 15 canonical tasks + 4 mediation chains in neurooracle.atoms.
  • [2026.05.15]: NeuroOracle launched: knowledge-graph explorer plus hypothesis engine with live demo at https://huggingface.co/spaces/zxcvb20001/NeuroOracle.
  • [2026.05.06]: Added 19 dataset and modality skills with companion scripts; all 86 skills enforce unified metadata (layer, skill_type, dependencies); skill_loader DAG validation ensures dependency graph correctness.
  • [2026.04.28]: Our technical report is now available on arXiv: https://arxiv.org/abs/2604.24696
  • [2026.04.22]: v1.0 released. Stable release with improvements and full documentation.
  • [2026.04.17]: Our project homepage is now live. Welcome to visit: https://cuhk-aim-group.github.io/NeuroClaw/
  • [2026.04.08]: NeuroBench released for multi-agent neuroimaging workflow evaluation.
  • [2026.04.02]: v0.1 released with complete NeuroClaw framework and core functionality.

✨ Key Features

NeuroClaw Framework Overview

πŸ”„ Data-Aware Orchestration

  • Dataset-Context Planning: Organize capabilities around dataset structure, metadata, and workflow stage instead of simply "which tool to call"
  • Automatic Skill Recommendation: Users specify the target dataset, and NeuroClaw recommends relevant skills and executable workflows
  • Preprocessing Constraint Awareness: Dataset-specific modality availability and preprocessing requirements are considered during orchestration

Supported Dataset Overview

Show supported dataset table
Dataset Supported Modalities Additional Data Cohort Scale Official Link
ABCD Study T1w; T2w; dMRI; rs-fMRI; task-fMRI Physical and mental health; substance use; culture/environment; neurocognition; biological data Target cohort of ~11,500 children; full cohort releases through the NIMH Data Archive https://abcdstudy.org/
ABIDE T1w; rs-fMRI ASD/control phenotypic data 1,112 datasets from 17 international sites https://fcon_1000.projects.nitrc.org/indi/abide/
ADHD-200 T1w; rs-fMRI Diagnostic status; ADHD symptom measures; demographics; medication history; QC measures 776 participants/datasets across 8 imaging sites https://fcon_1000.projects.nitrc.org/indi/adhd200/
AIBL T1w; PET (PiB, FDG, tau) Cognitive assessments; blood biomarkers; lifestyle and demographic data; APOE genotype ~1,100+ participants (healthy controls, MCI, AD) https://aibl.csiro.au/
AOMIC T1w; rs-fMRI; task-fMRI Personality traits (Big Five); fluid intelligence; demographic data ~1,000+ participants https://nilab-uva.github.io/AOMIC.github.io/
ADNI T1w; T2w; FLAIR; dMRI; rs-fMRI; PET Genetics/omics data; clinical and cognitive assessments ~2,000+ participants across ADNI phases https://adni.loni.usc.edu/
BOLD5000 T1w; task-fMRI Visual image stimuli; category and image metadata 4 participants with 5,000-image visual fMRI sessions https://bold5000-dataset.github.io/
Cam-CAN T1w; T2*w; rs-fMRI; task-fMRI; MEG Cognitive, sensory, and health measures across the adult lifespan ~700 participants ages 18-88 https://www.cam-can.org/
COBRE T1w; rs-fMRI Demographics; handedness; diagnostic information 147 participants: 72 schizophrenia patients and 75 healthy controls https://fcon_1000.projects.nitrc.org/indi/retro/cobre.html
DMT-HAR-MED rs-fMRI Psychedelic intervention conditions; behavioral and physiological measures 40 participants in OpenNeuro ds006644 https://openneuro.org/datasets/ds006644/versions/1.0.1
HBN T1w; T2w; dMRI; rs-fMRI; task-fMRI; EEG Psychiatric, behavioral, cognitive, lifestyle, genetics, actigraphy ~3,900+ released participants; target resource of at least 10,000 ages 5-21 https://fcon_1000.projects.nitrc.org/indi/cmi_healthy_brain_network/
HCP Aging T1w; T2w; dMRI; rs-fMRI; task-fMRI Behavioral, cognitive, health, and demographic measures ~700+ adults ages 36-100 https://www.humanconnectome.org/study/hcp-lifespan-aging
HCP Development T1w; T2w; dMRI; rs-fMRI; task-fMRI Behavioral, cognitive, health, and demographic measures ~600+ children and adolescents ages 5-21 https://www.humanconnectome.org/study/hcp-lifespan-development
HCP Early Psychosis T1w; T2w; dMRI; rs-fMRI; task-fMRI Diagnostic, clinical, behavioral, and cognitive measures ~250 early psychosis and control participants https://www.humanconnectome.org/study/hcp-early-psychosis
HCP Young Adult T1w; T2w; dMRI; rs-fMRI; task-fMRI Behavioral and cognitive measures ~1,200 young adult participants https://www.humanconnectome.org/study/hcp-young-adult
IXI T1w; T2w; MRA Healthy brain MRI from three London hospitals ~600 subjects https://brain-development.org/ixi-dataset/
MS Challenge T1w; T2w; FLAIR; PD Expert manual lesion segmentations for MS benchmarking 5 MS patients with multiple longitudinal timepoints https://smart-stats-tools.org/lesion-challenge
MND rs-fMRI; task-fMRI Motor neuron disease diagnosis and clinical measures 59 participants in OpenNeuro ds005874 https://openneuro.org/datasets/ds005874/versions/1.1.0
Natural Scenes Dataset T1w; task-fMRI Natural image stimuli; behavioral responses; image annotations 8 participants with dense repeated visual fMRI https://naturalscenesdataset.org/
NIFD T1w; fMRI; DTI; PET FTD clinical and cognitive data; UCSF Memory and Aging Center Frontotemporal dementia and related disorders cohorts https://ida.loni.usc.edu/
OASIS T1w; PET (PiB) Clinical and cognitive assessments; dementia diagnosis; demographic data Cross-sectional (400+) and longitudinal (150+) participants ages 18-96 https://www.oasis-brains.org/
PNC T1w; dMRI; ASL; rs-fMRI; task-fMRI Genotyping; clinical and neuropsychiatric assessment; Computerized Neurocognitive Battery >9,500 youth cohort; 1,445 participants with neuroimaging https://www.med.upenn.edu/bbl/philadelphianeurodevelopmentalcohort.html
PPMI T1w; rs-fMRI; DAT-SPECT; PET Clinical, genetic, biospecimen, and wearable sensor data for Parkinson's disease ~2,000+ participants across 30+ clinical sites worldwide https://www.ppmi-info.org/
REST-meta-MDD rs-fMRI MDD diagnosis; clinical and demographic measures 2,428 participants across 25 cohorts http://rfmri.org/REST-meta-MDD
SEED-IV EEG Emotion labels across four affective categories; trial-level session metadata 15 subjects across 3 sessions for emotion decoding benchmarks https://bcmi.sjtu.edu.cn/home/seed/
SEED-VIG EEG Vigilance/fatigue labels; continuous alertness annotations; behavioral metadata 23 subjects in sustained-attention driving-style vigilance recordings https://bcmi.sjtu.edu.cn/home/seed/
TCP rs-fMRI Psychiatric diagnostic interviews; cognitive and clinical assessments 245 transdiagnostic participants https://openneuro.org/datasets/ds004215
UCLA CNP T1w; dMRI; rs-fMRI; task-fMRI Diagnostic groups; neuropsychological and phenotypic assessments 272 participants in OpenNeuro ds000030 https://openneuro.org/datasets/ds000030
UK Biobank T1w; T2w; FLAIR; dMRI; rs-fMRI; task-fMRI Genotype/genomic data; questionnaires; hospital records; environmental data; sociodemographic data; physical measures ~50,000 participants with multimodal imaging data https://www.ukbiobank.ac.uk/

🎯 Executability and Reproducibility

  • Automatic Dependency Management: No manual installation needed; the system detects and resolves dependencies
  • True Model Execution: Beyond sharing docs, it guides and executes model reproduction
  • Environment Isolation: Virtual environments and containerization avoid system pollution
  • Verifiable Processes: Complete logging and result tracking
  • Shadow Checkpoints: Git-based filesystem snapshots for rollback and diff comparison without polluting the project repository
  • Subagent Orchestration: Spawns specialized subagents (biostatistician, clinical neuroscientist, methodology expert) for multi-perspective task execution
  • Reflective Learning: Automatic reflection on tool failures and task completion, with persistent memory for cross-session learning

🧠 End-to-End Research Coverage

  • Literature Review: arXiv search, PubMed retrieval, academic resource integration
  • Experiment Design: Scientific literature analysis, methodology evaluation, research proposal generation
  • Data Processing: Multi-format conversion (DICOM ↔ NIfTI), automated preprocessing pipelines
  • Model Execution: Run published research models, deep learning framework integration
  • Result Visualization: Scientific data visualization, statistical chart generation
  • Paper Writing: Auto-generated drafts, format standardization

🀝 Flexible Integration

  • NeuroClaw works as a standalone research assistant with its own GUI and CLI, so researchers can use it directly without depending on another host project.
  • skills/, materials/, USER.md, and SOUL.md can also be installed as a reusable skill library in existing agent systems such as OpenClaw, Hermes, and Claude Code.
  • The bundled core/ engine provides an integrated agent loop, skill loader, and tool runtime for standalone deployments.
  • Non-neuroscience connectors (WhatsApp, Telegram, Slack, calendar, e-commerce, SaaS auth) are disabled by default via core/config/features.json and can be re-enabled if needed.

πŸš€ Quick Start

Option 1. Desktop Client (recommended)

Download the latest Windows or macOS client from the GitHub Releases page.

  • Windows: use NeuroClaw Setup 0.2.1.exe for normal installation. The portable .exe is also available, but may take longer to start because it extracts the app first.
  • macOS: use the .dmg or .zip build from the release assets.
  • Open Settings to configure the model endpoint, runtime mode, Python path, FSL path, proxy, language, and text size.
  • Open NeuroOracle from the sidebar. If the graph file is missing, the client can download it from Hugging Face.

Linux remains supported through the source repository, command-line workflow, and web interface.

Option 2. Run from Source

Requirements: Python >= 3.10 and Git. Conda/Mamba, CUDA/GPU tools, FSL, FreeSurfer, and dcm2niix are optional depending on the workflows you want to run.

git clone https://github.com/CUHK-AIM-Group/NeuroClaw.git
cd NeuroClaw
python installer/setup.py
python core/agent/main.py --web

Then open http://localhost:7080 in your browser.

Useful checks:

python installer/setup.py --check
python core/agent/main.py --web --port 8080 --host 0.0.0.0

Settings are saved to neuroclaw_environment.json. API keys can be passed at runtime with --api-key or provided through the configured provider environment variable.

Option 3. Install as a Host-Agent Skill

Use this path if you want Codex, Claude Code, Cursor, or another coding agent to call NeuroClaw as a neuroimaging skill library.

git clone https://github.com/CUHK-AIM-Group/NeuroClaw.git
cd NeuroClaw
python installer/install_agent_integration.py --target codex

Common targets:

Host agent Install command
Codex python installer/install_agent_integration.py --target codex
Claude Code python installer/install_agent_integration.py --target claude-code
Cursor python installer/install_agent_integration.py --target cursor --scope project
Multiple agents python installer/install_agent_integration.py --target all

After installation, ask the host agent to use NeuroClaw or enter NeuroClaw mode for neuroimaging, NeuroOracle, NeuroBench, and autoresearch tasks.

NeuroClaw Feature Overview

Note: We provide benchmark run results and per-model outputs under materials/benchmark_results/. These artifacts can be used as practical references when running NeuroClaw benchmarks or reproducing model outputs.

Benchmark Evaluation

NeuroBench tasks live under neurobench/, and each task directory contains a task.md instruction file.

NeuroBench currently accepts these benchmark configurations:

  • with-skills: the agent can use the skills loaded from skills/
  • no-skills: the baseline run without skills
  • with-skills + no-skills paired comparison: enable --benchmark-compare-skills to run both variants for the same task set

Benchmark scoring is handled separately with --score-benchmark: it reads reports in output/, applies a GPT-5.4 weighted rubric, and generates numeric scores for planning completeness, tool/skill reasonableness, and command/code correctness. For fairness, each task case is scored in one batch across all comparable models to reduce scoring-standard drift. Skill-call counts are recorded separately and used for efficiency analysis.

To score existing benchmark reports:

python core/agent/main.py --score-benchmark

To speed up scoring on larger runs:

python core/agent/main.py --score-benchmark --score-workers 8

Web benchmark mode

python core/agent/main.py --web --benchmark

CLI benchmark batch runner

python core/agent/main.py --benchmark

To run the paired skill comparison in CLI mode:

python core/agent/main.py --benchmark --benchmark-compare-skills

In CLI benchmark mode, NeuroClaw will ask for:

  • the benchmark directory path
  • the benchmark model name

Then it will:

  • read all task.md files recursively from that directory
  • sort tasks alphabetically by task folder name
  • run tasks one by one without asking for intermediate confirmation
  • print progress in the terminal only
  • save reports under output/<model_name>/, with one markdown report per case and run

The benchmark reports include the solution thinking, skills used, skill-call counts, and the commands or code that were used or suggested.


πŸ“ Project Structure

NeuroClaw/
β”œβ”€β”€ README.md / README_zh.md        # Project documentation
β”œβ”€β”€ USER.md / SOUL.md               # User preferences and agent behavior guidelines
β”‚
β”œβ”€β”€ core/                           # Standalone NeuroClaw engine
β”‚   β”œβ”€β”€ agent/                      # CLI/Web agent entry points
β”‚   β”œβ”€β”€ web/                        # FastAPI Web UI
β”‚   β”œβ”€β”€ skill_loader/               # Reads skills/*/SKILL.md
β”‚   └── config/                     # Feature toggles and runtime settings
β”‚
β”œβ”€β”€ installer/                      # Setup wizard and host-agent integration installer
β”‚   β”œβ”€β”€ setup.py
β”‚   β”œβ”€β”€ config_wizard.py
β”‚   └── install_agent_integration.py
β”‚
β”œβ”€β”€ skills/                         # Skill library
β”‚   β”œβ”€β”€ base skills                 # Environment, search, BIDS, Git, conversion
β”‚   β”œβ”€β”€ interface skills            # Research idea, method design, experiments, writing
β”‚   └── subagent skills             # Tool, model, dataset, and modality workflows
β”‚
β”œβ”€β”€ models/                         # Brain model adapters and training/evaluation scripts
β”œβ”€β”€ neurooracle/                    # Knowledge graph and autoresearch pipeline
β”‚
β”œβ”€β”€ neurobench/                     # NeuroBench evaluation tasks (T01-T120)
β”‚
β”œβ”€β”€ docs/                           # Project website pages
β”œβ”€β”€ materials/                      # Research materials and benchmark outputs
β”‚
└── LICENSE                         # License

πŸ› οΈ Skill Quick Reference

Tip: Click the ℹ️ icon on any skill card in the Web UI to view expanded documentation, usage examples, and recent execution logs.

Base Layer

Skill Function Status
dcm2nii DICOM β†’ NIfTI conversion with metadata support βœ…
nii2dcm NIfTI β†’ DICOM conversion for clinical interoperability βœ…
git-essentials Core Git commands for collaboration βœ…
git-workflows Advanced Git workflows (rebase/worktree/bisect) βœ…
multi-search-engine Multi-engine web search without API keys βœ…
conda-env-manager Conda environment lifecycle management βœ…
docker-env-manager Docker environment management βœ…
dependency-planner Dependency planning and safe installation workflow βœ…
claw-shell Safe shell execution gateway via dedicated session βœ…
overleaf-skill Overleaf sync and collaborative manuscript operations βœ…
academic-research-hub Multi-source academic search and paper retrieval βœ…
bids-organizer Base skill for organizing raw data into BIDS structure βœ…
beautiful-log Export clean User/NeuroClaw dialogue into beautiful HTML logs βœ…
knowledge-graph-builder Build domain knowledge graphs from literature and databases βœ…
skill-updater Skill updater and management utilities βœ…

Interface Layer (Task Orchestration)

Skill Function Status
research-idea Brainstorms and generates research ideas from literature βœ…
method-design Formalizes network architecture and derives theoretical components βœ…
experiment-controller Finds and executes reproducible research experiments βœ…
paper-writing Generates hierarchical manuscript drafts from IDEA/METHOD/EXPERIMENT βœ…

Subagent Layer

Subagent in NeuroClaw includes four categories: tool, model, dataset, and modality.

Tool

Skill Function Status
brain-visualization Publication-ready figures and 3D assets (connectomes, atlas summaries, FreeSurfer PLY) βœ…
harmonization-tool Cross-site / cross-scanner feature harmonization (ComBat, ComBat-GAM, CovBat, site-as-covariate) with site-stratified and leave-site-out splitters; required for honest mega-analysis across multi-site cohorts βœ…
harness-core Core harness SDK: verification, checkpointing, drift detection, audit logging βœ…
mne-eeg-tool Base-layer MNE-Python implementation for EEG βœ…
fsl-tool FSL-based sMRI/fMRI/DWI processing utilities βœ…
fmriprep-tool fMRIPrep pipeline wrapper and execution βœ…
qsiprep-tool qsiPrep pipeline wrapper for diffusion MRI βœ…
hcppipeline-tool HCP-style processing pipeline utilities βœ…
dipy-tool Diffusion MRI processing via DIPY βœ…
nibabel-skill Low-level neuroimaging I/O and geometry handling (NIfTI, affine, FreeSurfer I/O) βœ…
nilearn-tool Fast neuroimaging feature extraction and decoding prep βœ…
conn-tool Functional connectivity computation and analysis βœ…
freesurfer-tool FreeSurfer-based MRI processing and segmentation βœ…

Model

Skill Function Status
run_models Model registry and model execution orchestration βœ…
wmh-segmentation White matter hyperintensity segmentation (MARS-WMH nnU-Net) βœ…
brain_gnn BrainGNN: graph neural network for fMRI classification βœ…
bnt BrainNetworkTransformer: dense FC Transformer with DEC pooling for phenotype prediction βœ…
combraintf Com-BrainTF: community-aware two-level Transformer over dense FC matrices βœ…
ibgnn IBGNN: interpretable PyG-based GNN with MLP message function and edge-mask explainer βœ…
lggnn LG-GNN: PyG-based GNN with Self-Attention Brain Pooling and mutual-information regularization βœ…
fm_app FM-APP: multi-stage phenotype prediction with fMRI+sMRI βœ…
neurostorm NeuroStorm: neuroimaging foundation model βœ…
glm Classical first-level and second-level GLM for task-fMRI activation and group inference βœ…
ica Resting-state network decomposition via independent component analysis βœ…
dictlearning Sparse resting-state network decomposition via dictionary learning βœ…
svm Classical neuroimaging disease classification with ROI/tabular features βœ…
spacenet Voxel-wise neuroimaging disease classification with sparse coefficient maps βœ…
kmeans Brain parcellation via K-means clustering βœ…
hierarchical Multi-scale brain parcellation via hierarchical clustering βœ…
filtering Temporal filtering for neuroimaging signal denoising βœ…
detrending Temporal drift removal for neuroimaging signal denoising βœ…

Dataset

Skill Function Status
abide-skill ABIDE dataset download, BIDS staging, and sMRI/rs-fMRI processing βœ…
aibl-skill AIBL dataset access, BIDS staging, and sMRI/PET processing βœ…
abcd-skill ABCD Study dataset download, BIDS staging, and multimodal processing βœ…
adhd200-skill ADHD-200 dataset download, BIDS staging, and sMRI/rs-fMRI processing βœ…
adni-skill ADNI dataset automated processing workflow βœ…
aomic-skill AOMIC dataset validation, BIDS staging, and sMRI/rs-fMRI/task-fMRI processing βœ…
bold5000-skill BOLD5000 dataset BIDS validation and visual task-fMRI processing βœ…
camcan-skill Cam-CAN dataset BIDS validation, multimodal sMRI/rs-fMRI/task-fMRI/dMRI processing βœ…
cobre-skill COBRE dataset BIDS staging and schizophrenia-control fMRI processing βœ…
dmt-har-med-skill DMT-HAR-MED dataset BIDS validation and psychedelic rs-fMRI processing βœ…
hbn-skill HBN dataset download, BIDS staging, and multimodal sMRI/fMRI/dMRI/EEG processing βœ…
hcpa-skill HCP Aging dataset download, BIDS staging, and multimodal sMRI/fMRI/dMRI processing βœ…
hcpd-skill HCP Development dataset download, BIDS staging, and multimodal sMRI/fMRI/dMRI processing βœ…
hcpep-skill HCP Early Psychosis dataset download, BIDS staging, and multimodal sMRI/fMRI/dMRI processing βœ…
hcpya-skill HCP Young Adult (HCP1200) dataset download, BIDS staging, and multimodal sMRI/fMRI/dMRI processing βœ…
ixi-skill IXI dataset BIDS validation and multimodal sMRI/MRA/dMRI processing βœ…
mnd-skill MND dataset BIDS validation, rs-fMRI/task-fMRI processing, and phenotype extraction βœ…
mschallenge-skill MS Lesion Challenge BIDS validation, lesion analysis, and longitudinal tracking βœ…
nsd-skill Natural Scenes Dataset BIDS validation, task-fMRI processing, and COCO stimulus extraction βœ…
nifd-skill NIFD dataset BIDS validation, multimodal sMRI/rs-fMRI/dMRI processing for frontotemporal dementia βœ…
oasis-skill OASIS dataset BIDS validation, sMRI processing, and phenotype extraction for aging/AD research βœ…
pnc-skill PNC dataset BIDS validation, multimodal sMRI/rs-fMRI/task-fMRI/dMRI processing for developmental studies βœ…
ppmi-skill PPMI dataset BIDS validation, multimodal sMRI/rs-fMRI/dMRI processing for Parkinson's disease βœ…
rest-mneta-mdd-skill REST-meta-MDD multi-site rs-fMRI processing, site harmonization, and depression phenotype extraction βœ…
seed-iv-skill SEED-IV EEG emotion recognition (4 emotions), feature extraction, and classification βœ…
seed-vig-skill SEED-VIG EEG vigilance/fatigue detection, feature extraction, and drowsiness classification βœ…
tcp-skill Transdiagnostic Connectome Project BIDS validation, multimodal sMRI/rs-fMRI/dMRI processing βœ…
ucla-cnp-skill UCLA CNP BIDS validation, multimodal sMRI/task-fMRI/dMRI processing, multi-disorder phenotyping βœ…
ukb-skill UKB brain imaging automated processing workflow βœ…

Modality

Skill Function Status
eeg-skill EEG preprocessing and feature extraction workflows βœ…
fmri-skill Functional MRI preprocessing and analysis workflows βœ…
smri-skill Structural MRI preprocessing and analysis workflows βœ…
dwi-skill Diffusion MRI preprocessing and analysis workflows βœ…
pet-skill PET imaging workflows (SUVR computation, reference regions, PVC) βœ…
asl-skill ASL perfusion MRI workflows (CBF quantification, Buxton model) βœ…
meg-skill MEG processing workflows (source localization, time-frequency, connectivity) βœ…

Legend: βœ… Implemented | πŸ—οΈ In Development | ⏳ Planned


πŸ™ Acknowledgments

Thanks to:

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