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The main organ of the human central nervous system, the human brain, is one of the most complex organs in the human body. The causes of many brain diseases and disorders, such as Alzheimer’s disease, and their ideal treatments are still not fully understood with the current medical technology. With medical imaging techniques such as magnetic resonance imaging (MRI), magnetoencephalography (MEG), and electroencephalography (EEG), the data obtained from these techniques can be used to study and examine brain diseases and disorders. This project focuses on utilizing a surface registration method on multiple brain surfaces to obtain various geometric transformations for brain studies, and the implementation of the analysis pipeline on a high performance computing (HPC) environment. Due to the infeasibility on runtime for performing surface registration between one template brain surface and multiple target brain surfaces, an approach to perform sub-surface extraction on each brain surface and computation on a HPC environment has been employed. This has allowed a significant reduction in runtime and has also allowed the results to be obtained within reasonable time.

This report outlines the design and testing of an olfactory stimulus in an fMRI setting. The goal of this project was to create a device that would be both cost effective and compatible with an extremely unique environment. The sense of smell provides a unique challenge for scientists. Because of most of the processing goes on in the deeper centers of the brain, it can be often hard to image. Another issue with the study of olfaction is the actual delivery of the odour. This problem is what our device was designed to solve. We went through many prototypes which had several drawbacks, whether they were price or compatibility. In the end we decided to go with a device that was pneumatically controlled and involved the use of a Laerdal mask. This device provided an air tight mechanism to deliver smell into the MRI environment, without having to worry about passing signals in and out, which can be challenging. The system was fairly simple but proved very effective. The overall result was activation seen in expected regions of the brain.

This paper serves to understand if there can be a difference in the brain activity of a professional dancer and an unprofessional dancer. First, a general comparison is made between music and dance to show how they are related and why dance is associated with music often. Secondly, the relationship between brain activity and music will be discussed, and then the relationship between Dance and brain activity are broken down into three subtopics: timing, rhythm, and spatial organization in order to explain why people dance and how dance can be a sequentially planned series of movement. To conclude the research, music, dance, and brain activity are related altogether to different brain regions to understand why dance occurs and how its subsequent movements occur. Listening to music requires at least three basic motor control functions: timing, sequencing, and spatial organisation of movement. These functions mediate complex behaviors controlled and interpreted by several cortical regions, subcortical regions, motor areas, and most importantly, mirror neurons by converting incoming sensory information into motor instructions and actions.

HIGHLIGHTS AxonPacking: Open-source software for simulating white matter microstructure.Validation on a theoretical disk packing problem.Reproducible and stable for various densities and diameter distributions.Can be used to study interplay between myelin/fiber density and restricted fraction.Quantitative Magnetic Resonance Imaging (MRI) can provide parameters that describe white matter microstructure, such as the fiber volume fraction (FVF), the myelin volume fraction (MVF) or the axon volume fraction (AVF) via the fraction of restricted water (fr). While already being used for clinical application, the complex interplay between these parameters requires thorough validation via simulations. These simulations required a realistic, controlled and adaptable model of the white matter axons with the surrounding myelin sheath. While there already exist useful algorithms to perform this task, none of them combine optimisation of axon packing, presence of myelin sheath and availability as free and open source software. Here, we introduce a novel disk packing algorithm that addresses these issues. The performance of the algorithm is tested in term of reproducibility over 50 runs, resulting density, and stability over iterations. This tool was then used to derive multiple values of FVF and to study the impact of this parameter on fr and MVF in light of the known microstructure based on histology sample. The standard deviation of the axon density over runs was lower than 10−3 and the expected hexagonal packing for monodisperse disks was obtained with a density close to the optimal density (obtained: 0.892, theoretical: 0.907). Using an FVF ranging within [0.58, 0.82] and a mean inter-axon gap ranging within [0.1, 1.1] μm, MVF ranged within [0.32, 0.44] and fr ranged within [0.39, 0.71], which is consistent with the histology. The proposed algorithm is implemented in the open-source software AxonPacking (https://github.com/neuropoly/axonpacking) and can be useful for validating diffusion models as well as for enabling researchers to study the interplay between microstructure parameters when evaluating qMRI methods.

Chronic systemic inflammatory conditions, such as atherosclerosis, diabetes and obesity are associated with increased risk of stroke, which suggests that systemic inflammation may contribute to the development of stroke in humans. The hypothesis that systemic inflammation may induce brain pathology can be tested in animals, and this was the key objective of the present study. First, we assessed inflammatory changes in the brain in rodent models of chronic, systemic inflammation. PET imaging revealed increased microglia activation in the brain of JCR-LA (corpulent) rats, which develop atherosclerosis and obesity, compared to the control lean strain. Immunostaining against Iba1 confirmed reactive microgliosis in these animals. An atherogenic diet in apolipoprotein E knock-out (ApoE−/−) mice induced microglial activation in the brain parenchyma within 8 weeks and increased expression of vascular adhesion molecules. Focal lipid deposition and neuroinflammation in periventricular and cortical areas and profound recruitment of activated myeloid phagocytes, T cells and granulocytes into the choroid plexus were also observed. In a small, preliminary study, patients at risk of stroke (multiple risk factors for stroke, with chronically elevated C-reactive protein, but negative MRI for brain pathology) exhibited increased inflammation in the brain, as indicated by PET imaging. These findings show that brain inflammation occurs in animals, and tentatively in humans, harbouring risk factors for stroke associated with elevated systemic inflammation. Thus a “primed” inflammatory environment in the brain may exist in individuals at risk of stroke and this can be adequately recapitulated in appropriate co-morbid animal models.

We introduce Sleep, a new Python open-source graphical user interface (GUI) dedicated to visualization, scoring and analyses of sleep data. Among its most prominent features are: (1) Dynamic display of polysomnographic data, spectrogram, hypnogram and topographic maps with several customizable parameters, (2) Implementation of several automatic detection of sleep features such as spindles, K-complexes, slow waves, and rapid eye movements (REM), (3) Implementation of practical signal processing tools such as re-referencing or filtering, and (4) Display of main descriptive statistics including publication-ready tables and figures. The software package supports loading and reading raw EEG data from standard file formats such as European Data Format, in addition to a range of commercial data formats. Most importantly, Sleep is built on top of the VisPy library, which provides GPU-based fast and high-level visualization. As a result, it is capable of efficiently handling and displaying large sleep datasets. Sleep is freely available (http://visbrain.org/sleep) and comes with sample datasets and an extensive documentation. Novel functionalities will continue to be added and open-science community efforts are expected to enhance the capacities of this module.

This Neuroimaging data management plan (DMP) template is designed to be completed in two phases: Phase 1 questions probe at a high-level, seeking information about the general direction of the study. Normally, researchers will be able to respond to phase 1 questions at the outset of a project. Phase 2 questions seek greater detail. It is understood that these answers will often depend on the outcome of several steps in the research project, such as: a literature review, imaging protocol design and experimental design, or running multiple pilot subjects and interpreting the outcome. As these details become known, the DMP can and should be revisited. This approach underscores that DMPs are living documents that evolve throughout a research project.

Olfaction is an ancient and complex chemosensory process that for many animals serves as their main sensory link with the surrounding environment. In the field of functional brain imaging, it is a process that has been largely unstudied due to many complicating factors such as the qualitative nature of olfaction, the difficulty of providing stimuli in a controlled manner, and the non-superficial location of the main olfactory centers of the brain. The goal of this project was to develop an MRI compatible device for generation and presentation of olfactory stimulus for use in functional imaging of the olfactory response. After taking into consideration various constraints in the design process, the final device design consists of a scented liquid that is nebulised in an Erlenmeyer flask by pressurized medical air and subsequently transported through chemically inert tubing to a modified ventilator mask secured to the subject. To test the device, functional magnetic resonance imaging (fMRI) analysis was performed with an experimental protocol that provided stimulus for a period of 30 seconds and allowed it to clear for 90 seconds. This procedure was repeated over 5 cycles starting with 90 seconds of no stimulus resulting in a total time of 10 minutes. Statistical analysis was performed on the resulting images from two of the three fMRI experiments undertaken and the results of the last trial show activation of deep areas of the brain commonly associated with olfaction and described in existing publications on the topic. This is a promising result given the number of trials undertaken and the simplistic nature of the overall experimental protocol. Therefore, the conclusion is that with increased time and funding the basic device and experimental protocols presented in this project could easily be expanded to assist in a functional characterization of the olfactory response.

{"references": ["Harel et al., (2023). Open design and validation of a reproducible videogame controller for MRI and MEG."]} Full documentation and files required to build the CNeuromod controller.