Skill Claude CodeCodex
Use this workflow skill whenever the user wants to turn connectome-model outputs into network discoveries: compare aligned brain maps, compute permutation significance, rank neuromodulation targets, summarize atlas-level effects, or combine CPM with spatial interpretation. Triggers include 'connectome discovery'…
Skill Claude CodeCodex
Use this model skill whenever the user wants Connectome Predictive Modeling with fold-local functional-connectivity edge selection for classification or regression. Triggers include 'CPM', 'connectome predictive modeling', 'functional connectivity prediction', 'positive network', 'negative network', and 'edge…
Skill Claude CodeCodex
Use this skill whenever the user wants to convert DICOM files or folders to NIfTI format (.nii or .nii.gz), extract neuroimaging volumes from clinical DICOM series (MRI, CT, PET, etc.), prepare raw DICOM data for research processing pipelines, anonymize while converting, or batch-convert multiple series/studies.…
Skill Claude CodeCodex
Use this skill whenever a NeuroClaw skill, model, or sub-agent reports a missing dependency (e.g. ImportError, ModuleNotFoundError, command not found), or when the user explicitly requests to install, setup, configure, or fix any library, package, compiler, CUDA toolkit, conda environment, system tool, or git-based…
Skill Claude CodeCodex
Use this model doc whenever the user wants to perform neuroimaging signal denoising with classical detrending methods. This is a non-deep-learning preprocessing route focused on removing low-frequency drift and linear trends from time series before downstream analysis.
Skill Claude CodeCodex
Use this model doc whenever the user wants to perform resting-state network decomposition using DictLearning. This is a non-deep-learning unsupervised route focused on sparse component extraction, network map discovery, and subject-level time series from resting-state fMRI.
Skill Claude CodeCodex
Use this skill whenever any NeuroClaw diffusion MRI / DWI modality skill needs to execute concrete DIPY operations: load DWI (NIfTI+bvals+bvecs), optional masking, DTI fitting, compute FA/MD/AD/RD, and extract ROI statistics. This is the dedicated base/tool skill that contains all specific DIPY code and usage…
Skill Claude CodeCodex
Use this skill whenever the user wants an end-to-end workflow for the DMT-HAR-MED dataset (ds006644), including download, BIDS organization, and processing of rs-fMRI data from a psychedelic intervention study. Triggers include: 'DMT-HAR-MED', 'DMT HAR MED', 'ds006644', 'process DMT data', 'psychedelic fMRI', or any…
Skill Claude CodeCodex
Use this skill whenever the user wants to pull, run, build, compose, list, prune, manage, or otherwise handle Docker containers, images, volumes, networks, or Docker Compose projects, or when a NeuroClaw skill (e.g. wmh-segmentation, freesurfer-processor in container mode) requires a clean, isolated, GPU-enabled…
Skill Claude CodeCodex
Use this skill whenever the user wants to preprocess diffusion MRI / DWI data, compute diffusion metrics (FA/MD/AD/RD, etc.), extract ROI-wise diffusion features, or run tractography/connectome-related workflows. Triggers include: 'DWI', 'DTI', 'diffusion MRI', 'FA', 'MD', 'AD', 'RD', 'eddy', 'topup', 'QSIPrep'…
Skill Claude CodeCodex
Use this skill whenever the user wants to load, preprocess, epoch, filter, or extract features from EEG data (resting-state, task-based, BCI, clinical, motor imagery, emotion, epilepsy, fatigue, etc.). Triggers include: 'eeg', 'EEG preprocessing', 'EEG feature extraction', 'band power', 'downsample to frequency…
Skill Claude CodeCodex
Use this skill whenever the user wants to execute experiments based on a finalized method and record results. Triggers include: 'run experiment', 'experiment controller', 'implement experiment', 'run model', 'execute training', 'experiment-controller', 'record results', 'ablation study', or any request to turn…
Skill Claude CodeCodex
Use this model doc whenever the user wants to perform neuroimaging signal denoising with classical temporal filtering methods. This is a non-deep-learning preprocessing route focused on temporal cleaning, frequency selection, and preparation of cleaner time series for downstream analysis.
Skill Claude CodeCodex
Use this model doc whenever the user wants to run FM-APP for phenotype prediction using fMRI ROI features and optional sMRI features. This document provides model-level usage and delegates preprocessing to fmri-skill and smri-skill.
Skill Claude CodeCodex
Use this skill whenever the user wants to perform fMRI preprocessing, first-level analysis, ROI extraction, functional connectivity, effective connectivity, or atlas-based alignment to MNI152 space using either fMRIPrep, HCP-style pipelines, or CONN Toolbox. Triggers include: 'fmri', 'fMRI analysis', 'functional…
Skill Claude CodeCodex
Use this skill whenever the user wants to perform standardized preprocessing of functional MRI (fMRI) and anatomical MRI data using fMRIPrep. Triggers include: 'fmriprep', 'fMRIPrep', 'fMRI preprocessing', 'BIDS fMRI', 'run fmriprep', 'preprocess bold', 'BOLD preprocessing', 'anatomical preprocessing', or any request…
Skill Claude CodeCodex
Use this skill whenever the user wants to process structural MRI data (T1w, T2w, FLAIR, etc.) with FreeSurfer, especially for cortical/subcortical segmentation, surface reconstruction, parcellation, cortical thickness, volume statistics, or full recon-all pipeline. Triggers include: 'freesurfer', 'recon-all', 'segment…
Skill Claude CodeCodex
Use this skill whenever the user wants to process neuroimaging data with FSL (FMRIB Software Library), covering structural MRI, functional MRI (fMRI), and diffusion MRI (dMRI/DTI). Triggers include: 'use FSL', 'FSL processing', 'fslanat', 'FEAT', 'MELODIC', 'eddy', 'bedpostx', 'probtrackx', 'BET', 'FAST', 'FLIRT'…
Skill Claude CodeCodex
Essential Git commands and workflows for version control, branching, and collaboration.
Skill Claude CodeCodex
Advanced git operations beyond add/commit/push. Use when rebasing, bisecting bugs, using worktrees for parallel development, recovering with reflog, managing subtrees/submodules, resolving merge conflicts, cherry-picking across branches, or working with monorepos.
Skill Claude CodeCodex
Use this model doc whenever the user wants to run a classical General Linear Model (GLM) for task-evoked fMRI activation analysis. This is a non-deep-learning model route focused on design matrices, first-level/second-level statistics, and statistical maps.
Skill Claude CodeCodex
Use this skill whenever the user wants to remove site/scanner/batch effects from neuroimaging features before running downstream models, run mega-analysis across multiple datasets, or evaluate models with leave-site-out / site-stratified protocols. Triggers include: 'harmonize', 'ComBat', 'CovBat', 'site effect'…
Skill Claude CodeCodex
Core harness library providing standardized self-verification, checkpoint management, drift detection, and audit logging utilities for all NeuroClaw skills. This is NOT directly called by users; instead, it is imported as a Python module by other skills for harness-compliant execution, validation, and reproducibility.…
Skill Claude CodeCodex
Use this skill whenever the user wants an end-to-end workflow for the Healthy Brain Network (HBN) dataset, including download, BIDS organization, and multimodal processing of sMRI, dMRI, rs-fMRI, task-fMRI, and EEG data. Triggers include: 'HBN', 'Healthy Brain Network', 'process HBN', 'HBN fMRI', 'HBN EEG', or any…