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.