micapipe

micapipe processes multimodal MRI datasets to extract and summarize brain microstructure, cortical geometry, functional connectivity, and structural connectivity across multiple spatial scales for human neuroimaging studies.

Key Features:

• Integration Across Modalities: Processes MRI data conforming to the Brain Imaging Data Structure (BIDS) format to integrate multiple imaging modalities.
• Connectome Generation: Generates structural connectomes using diffusion tractography and functional connectomes using resting-state signal correlations.
• Geodesic Distance Matrices: Computes cortico-cortical geodesic distance matrices to quantify cortical proximity.
• Microstructural Profile Covariance: Computes microstructural profile covariance matrices to assess inter-regional similarity in cortical myelin proxies.
• Spatial Scale Flexibility: Supports 18 established cortical parcellations ranging from 100 to 1,000 parcels and includes subcortical and cerebellar parcellations.
• Surface Space Representation: Represents outputs on native, conte69, and fsaverage5 surface spaces.
• Quality Control: Provides processed outputs that can be quality controlled at individual and group levels.

Scientific Applications:

• Integrative Multimodal Analysis: Enables combined analysis of brain microstructure, morphology, function, and connectivity using multimodal MRI data.
• Anatomical Studies: Supports basic anatomical investigations of cortical organization and myelination patterns.
• Network and Functional Investigations: Facilitates analyses of neural networks and their functional implications using structural and functional connectomes.

Methodology:

Processes BIDS-formatted MRI data; performs diffusion tractography for structural connectomes and resting-state correlation for functional connectomes; computes geodesic distance matrices and microstructural profile covariance matrices from cortical myelin proxies; supports 18 cortical parcellations (100–1,000 parcels) plus subcortical and cerebellar parcellations and outputs on native, conte69, and fsaverage5 surface spaces; includes individual- and group-level quality control.