Skill Claude CodeCodex
Use this skill whenever the user wants an end-to-end workflow for the ABCD Study dataset, including controlled access through the NIH Brain Development Cohorts (NBDC) platform, BIDS organization, and multimodal processing of sMRI, fMRI, and dMRI. Triggers include: 'ABCD Study', 'ABCD data', 'process ABCD', 'ABCD…
Skill Claude CodeCodex
Use this skill whenever the user wants an end-to-end workflow for the ABIDE (Autism Brain Imaging Data Exchange) dataset, including download, BIDS organization, and processing of sMRI and rs-fMRI data. Triggers include: 'ABIDE', 'ABIDE data', 'process ABIDE', 'ABIDE fMRI', 'ABIDE sMRI', 'autism imaging', or any…
Skill Claude CodeCodex
Use this skill when users need to search academic papers, download research documents, extract citations, or gather scholarly information. Triggers include: requests to "find papers on", "search research about", "download academic articles", "get citations for", or any request involving academic databases like arXiv…
Skill Claude CodeCodex
Use this skill whenever the user wants an end-to-end workflow for the ADHD-200 dataset, including download, BIDS organization, and processing of sMRI and rs-fMRI data. Triggers include: 'ADHD-200', 'ADHD200', 'process ADHD data', 'ADHD fMRI', or any request to run the ADHD-200 pipeline. This is the NeuroClaw…
Skill Claude CodeCodex
Use this skill whenever the user wants an end-to-end workflow for ADNI or ADNI-DOD data, including controlled LONI IDA access, BIDS preparation, fMRIPrep preprocessing, and DK68 ROI processing. Trigger on ADNI, ADNI-DOD, ADNIDOD, DoD-ADNI, SCRNO, or ADNI imaging requests.
Skill Claude CodeCodex
Use this skill whenever the user wants an end-to-end workflow for the AIBL (Australian Imaging, Biomarkers and Lifestyle) dataset, including data access guidance, BIDS organization, and multimodal processing of sMRI and PET (PiB, FDG, tau). Triggers include: 'AIBL', 'AIBL data', 'process AIBL', 'AIBL PET', 'AIBL MRI'…
Skill Claude CodeCodex
Use this skill whenever the user wants an end-to-end workflow for the AOMIC (Amsterdam Open MRI Collection) dataset, including data access, BIDS organization, and multimodal processing of sMRI, rs-fMRI, and task-fMRI. Triggers include: 'AOMIC', 'AOMIC data', 'process AOMIC', 'AOMIC fMRI', 'AOMIC resting state', or any…
Skill Claude CodeCodex
Use this skill whenever the user wants to process Arterial Spin Labeling (ASL) perfusion MRI data including CBF (cerebral blood flow) quantification, ASL preprocessing (motion correction, partial volume correction, M0 normalization), or ASL-based brain perfusion analysis. Triggers include: 'ASL', 'ASL processing'…
Skill Claude CodeCodex
Use this skill after a conversation or task is completed when the user wants a clean, beautiful HTML chat log. It keeps only direct NeuroClaw User dialogue, filters out tool calls / internal traces / SKILL.md reading notes, and renders distinct colored message cards for each side.
Skill Claude CodeCodex
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'…
Skill Claude CodeCodex
Use this model doc whenever the user wants to run BrainNetworkTransformer for fMRI phenotype prediction, including data loading, training, and evaluation. BNT uses dense FC matrices (no PyG dependency) with DEC pooling + interpretable transformer encoder.
Skill Claude CodeCodex
Use this skill whenever the user wants an end-to-end workflow for the BOLD5000 dataset, including download, BIDS organization, and processing of task-fMRI data with visual image stimuli. Triggers include: 'BOLD5000', 'BOLD 5000', 'process BOLD5000', 'visual fMRI', or any request to run the BOLD5000 pipeline. This is…
Skill Claude CodeCodex
Use this skill whenever the user wants brain-age prediction, predicted-age bias correction, Brain-PAD/brain-age gap export, cross-validated age modeling, or downstream group analysis of accelerated or delayed brain aging. Triggers include 'brain age', 'Brain-PAD', 'brain age gap', 'predicted age', 'age bias…
Skill Claude CodeCodex
Use this skill whenever the user wants to visualize neuroimaging analysis results, including 3D brain connectivity networks, atlas-based regional activation summaries, or FreeSurfer cortical surface meshes with anatomical colors. Triggers include: 'brain visualization', 'visualize connectome', '3D brain network'…
Skill Claude CodeCodex
Use this model doc whenever the user wants to run BrainGNN for fMRI phenotype prediction, including graph construction, training, and evaluation. This document focuses on model-level usage and delegates upstream preprocessing to fmri-skill (and optionally hcpya-skill for HCP data).
Skill Claude CodeCodex
Use this model skill whenever the user wants to train, evaluate, or apply BrainNetCNN to dense ROI-by-ROI structural or functional connectivity matrices for neuroimaging classification or regression. Triggers include 'BrainNetCNN', 'edge-to-edge convolution', 'connectome CNN', 'FC matrix CNN', 'brain network…
Skill Claude CodeCodex
Use this skill whenever the user wants an end-to-end workflow for the Cam-CAN (Cambridge Centre for Ageing and Neuroscience) dataset, including BIDS validation, multimodal processing of sMRI, rs-fMRI, task-fMRI, and MEG, phenotype extraction, and QC integration. Triggers include: 'Cam-CAN', 'CamCAN', 'process Cam-CAN…
Skill Claude CodeCodex
Use this skill whenever the scientific target is a treatment effect rather than ordinary outcome prediction: propensity weighting, S/T/X learners, doubly robust learning, policy learning, causal forests, TARNet, DragonNet, CATE estimation, heterogeneous treatment effects, and individualized treatment selection.…
Skill Claude CodeCodex
Use this skill whenever any NeuroClaw skill, sub-agent, or model needs to execute shell commands safely (e.g. source environment scripts, run recon-all, git operations, conda commands, ls, cat logs, etc.). Triggers include: 'run shell', 'execute command', 'shell command', 'tmux claw', 'run in claw session', 'safe…
Skill Claude CodeCodex
Use this model skill whenever the user wants a compact residual 3D convolutional neural network for voxel-level classification or regression from structural MRI, functional MRI summaries, statistical maps, or other aligned volumetric neuroimaging data. Triggers include 'CNN3D', '3D CNN', 'voxel model', 'volumetric…
Skill Claude CodeCodex
Use this skill whenever the user wants an end-to-end workflow for the COBRE dataset, including download, BIDS organization, and processing of sMRI and rs-fMRI data for schizophrenia research. Triggers include: 'COBRE', 'process COBRE', 'COBRE schizophrenia', 'COBRE fMRI', or any request to run the COBRE pipeline. This…
Skill Claude CodeCodex
Use this model doc whenever the user wants to run Com-BrainTF (Community-aware Brain Transformer) for fMRI phenotype prediction. Com-BrainTF uses dense FC matrices with a two-level Transformer (per-community local + global) and DEC pooling. NeuroClaw auto-derives community partitions from atlas naming conventions (Yeo…
Skill Claude CodeCodex
Use this skill whenever the user wants to create, activate, list, export, update, clone, remove, or otherwise manage conda environments, or when a deep-learning / model skill requires a clean, isolated conda environment (e.g. 'create conda env for torch 2.3 cuda', 'export current env to yml', 'list all my conda envs'…
Skill Claude CodeCodex
Use this skill whenever the user wants to perform advanced functional connectivity (ROI-to-ROI, seed-to-voxel, ICA) or effective connectivity (PPI, gPPI, DCM) analysis using the CONN Toolbox. Triggers include: 'conn', 'CONN toolbox', 'functional connectivity', 'effective connectivity', 'ROI-to-ROI', 'seed-to-voxel'…