LayNii

LayNii performs layer-specific analysis of high-resolution (sub-millimeter) functional MRI data to resolve cortical layers and columns, support VASO and GE-BOLD analyses, and mitigate artifacts for accurate spatial mapping of neural activity.

Key Features:

• Layer-Specific Analysis: Targets sub-millimeter layer-fMRI data, addressing low signal-to-noise ratio (SNR) and restricted coverage with command-line executables implemented in C/C++.
• Layerification and Columnarization: Performs layerification and columnarization directly in native voxel space to localize neural activity across cortical depth and columns.
• Layer-Specific Smoothing: Implements smoothing methods tailored to preserve layer-specific signals while reducing noise.
• Artifact Mitigation: Provides model-based vein mitigation for GE-BOLD data and addresses image blurring and distortions to improve spatial accuracy.
• Quality Assessment: Includes tools for quality assessment of artifact-dominated sub-millimeter fMRI data.
• VASO Analysis: Supports analysis of VASO (Vascular Space Occupancy) data to examine cerebral blood volume changes.

Scientific Applications:

• Microstructural Organization: Investigating cortical microstructure by resolving activity across layers and columns.
• Cortical Processing and Directional Information Flow: Studying layer-specific processing and directional information flow within and across neural circuits.
• Neural Connectivity Mapping: Mapping fine-grained functional connectivity across cortical depths.
• High-Resolution BOLD and VASO Studies: Enabling GE-BOLD and VASO experiments that require venous-artifact mitigation and high spatial precision.

Methodology:

Layerification and columnarization in native voxel space; layer-specific smoothing; model-based vein mitigation for GE-BOLD; quality-assessment measures for sub-millimeter fMRI; VASO data analysis; implemented as C/C++ command-line executables.