hierarchical

Generates data-driven brain parcellations from neuroimaging features using hierarchical clustering.

89|5|Updated Mar 25, 2026
One-click install
npx skills add https://github.com/CUHK-AIM-Group/NeuroDiscovery --skill hierarchical-cuhk-aim-group
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: hierarchical
Source: https://github.com/CUHK-AIM-Group/NeuroDiscovery/tree/main/skills/hierarchical
Command: npx skills add https://github.com/CUHK-AIM-Group/NeuroDiscovery --skill hierarchical-cuhk-aim-group

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires nilearn.

What problem does it solve? Researchers who want to partition the brain into data-driven parcels rather than rely on a predefined atlas need a reproducible unsupervised route. This Skill provides model-level guidance for running hierarchical (agglomerative/Ward) clustering on neuroimaging features to produce parcel label maps and cluster summaries. ## Core Features & Use Cases - Data-driven parcellation: Partitions voxels, vertices, or ROI features into brain parcels from functional or structural similarity. - Multi-scale outputs: Exports parcel label maps, cluster size summaries, and optional dendrogram or merge information across scales. - Workflow delegation: Coordinates with fmri-skill and smri-skill for feature preparation and nilearn-tool for concrete masking, feature matrices, and parcel export. - Use Case: A researcher with preprocessed resting-state fMRI data wants a 200-parcel group-level parcellation; this Skill guides feature preparation, Ward clustering, and label map export. ## Quick Start Ask the agent to run hierarchical clustering parcellation on your preprocessed fMRI images with a group mask and a target of 200 parcels, exporting the label map to the output directory.

Frequently Asked Questions about hierarchical

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I perform brain parcellation with hierarchical clustering?▼

Prepare a preprocessed feature matrix or aligned image list with an optional brain mask, then fit agglomerative or Ward-style hierarchical clustering with a target parcel count. The workflow exports a parcel label map and cluster size summaries.

What is hierarchical clustering used for in neuroimaging?▼

Hierarchical clustering partitions voxels, vertices, or ROI features into data-driven brain parcels based on functional or structural similarity. It is used to build subject-level or group-level parcellations for downstream connectivity, decoding, or visualization.

Hierarchical clustering vs predefined atlas for brain parcellation?▼

Hierarchical clustering derives parcels directly from your data rather than imposing a fixed atlas, capturing cohort-specific organization and multi-scale structure. However, data-driven parcels may vary across cohorts and may not align with standard atlases.

What inputs does hierarchical brain parcellation require?▼

It requires a preprocessed feature matrix or aligned neuroimaging image list and a target parcel count. Optional inputs include a brain mask, connectivity or similarity matrix, spatial adjacency constraints, and linkage parameters.

What are the limitations of hierarchical clustering parcellation?▼

Results depend strongly on preprocessing, feature definition, and spatial normalization quality. It is computationally expensive for large voxel spaces, and parcellations may not be stable or comparable across different cohorts.