Abstract
High-resolution fMRI in the sub-millimeter regime allows researchers to resolve brain activity across cortical layers and columns non-invasively. While these high-resolution data make it possible to address novel questions of directional information flow within and across brain circuits, the corresponding data analyses are challenged by MRI artifacts, including image blurring, image distortions, low SNR, and restricted coverage. These challenges often result in insufficient performance accuracy of conventional analysis pipelines. Here we introduce a new software suite that is specifically designed for layer-specific functional MRI: LAYNII. This toolbox is a collection of commandline executable programs written in C/C++ and is distributed open-source and as pre-compiled binaries for Linux, Windows, and macOS. LAYNII is designed for layer-fMRI data that suffer from SNR and coverage constraints and thus cannot be straight-forwardly analysed in alternative software packages. Some of the most popular programs of LAYNII contain ‘layerification’ and columnarization in the native voxel space of functional data as well as many other layer-fMRI specific analysis tasks: layer-specific smoothing, vein-removal of GE-BOLD data, quality assessment of artifact dominated sub-millimeter fMRI, as well as analyses of VASO data.
Highlights
A new software toolbox is introduced for layer-specific functional MRI: LAYNII.
LAYNII is a suite of command-line executable C++ programs for Linux, Windows, and macOS.
LAYNII is designed for layer-fMRI data that suffer from SNR and coverage constraints.
LAYNII performs layerification in the native voxel space of functional data.
LAYNII performs layer-smoothing, GE-BOLD vein removal, QA, and VASO analysis.
Competing Interest Statement
Author OFG and RG work for Brain Innovation and have financial interest tied to the company.
Footnotes
1 The name has nothing to do with the author’s wife’s pet name: Leni, nor does it relate to the kissable laynii: https://www.urbandictionary.com/laynii.
