Kabir Arora’s research while affiliated with Maastricht University and other places

Foreword from the editors. We hosted four keynote speakers: Wolf Singer, Bill Bialek, Danielle Bassett, and Sonja Gruen. They enlightened us about computations in the cerebral cortex, the reduction of high-dimensional data, the emerging field of computational psychiatry, and the significance of spike patterns in motor cortex. From the submissions, we also selected four featured orals as particularly noteworthy. They discussed a new role for cortical oscillations as a tempering mechanism, branch-specific computations in Purkinje cells, low frequency entrainment in processing sign language, and decreasing neural heterogeneity as a unifying sign of epilepsy. An additional 16 submissions were selected for shorter oral presentation in the plenary sessions, touching subjects such a spike and population coding, neural computation and interaction, astrocytic and dopaminergic modulation of plasticity, several kinds of sensory processing, reward learning, respiratory and motor control, neural activity propagation and synchronization, and brain organization in epilepsy and schizophrenia. We were also very pleased by the quality of the 213 presented posters, which drew a strong attendance, and the resulting online interactions between presenters and attendees. The full breadth of computational neuroscience was represented, from theory and method development over data analysis to applications.

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 spatial 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 command-line executable programs written in C/C++ and is distributed opensource 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 straightforwardly analyzed 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: layerspecific smoothing, model-based vein mitigation of GE-BOLD data, quality assessment of artifact dominated sub-millimeter fMRI, as well as analyses of VASO data.

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. Graphical abstract