• Neuroinformatics

This dataset contains EEG and fMRI data of the same subjects in a simultaneous EEG-fMRI session and a separate EEG-fMRI session. The corresponding paper is published in Frontiers of Neuroscience - Brain Imaging Methods.

Temporally independent functional modes (TFMs) are functional brain networks identified based on their temporal independence. The rationale behind identifying TFMs is that different functional networks may share a common anatomical infrastructure yet display distinct temporal dynamics. Extracting TFMs usually require a larger number of samples than acquired in standard fMRI experiments, and thus have therefore previously only been performed at the group level. Here, using an ultra-fast fMRI sequence, MESH-EPI, with a volume repetition time of 158 ​ms, we conducted an exploratory study with n ​= ​6 subjects and computed TFMs at the single subject level on both task and resting-state datasets. We identified 6 common temporal modes of activity in our participants, including a temporal default mode showing patterns of anti-correlation between the default mode and the task-positive networks, a lateralised motor mode and a visual mode integrating the visual cortex and the visual streams. In alignment with other findings reported recently, we also showed that independent time-series are largely free from confound contamination. In particular for ultra-fast fMRI, TFMs can separate the cardiac signal from other fluctuations. Using a non-linear dimensionality reduction technique, UMAP, we obtained preliminary evidence that combinations of spatial networks as described by the TFM model are highly individual. Our results show that it is feasible to measure reproducible TFMs at the single-subject level, opening new possibilities for investigating functional networks and their integration. Finally, we provide a python toolbox for generating TFMs and comment on possible applications of the technique and avenues for further investigation.

These videos contain samples of visual stimuli used in an fMRI study on top-down feedback across cortical depths in human early visual cortex [in preparation]. There is one video sample for each of the three experimental conditions in the main experiment: ‘Pac-Man dynamic’, ‘Pac-Man static’, and ‘control dynamic’. In addition, there are videos of stimuli used in a control experiment in which the shape of the stimulus (‘Pac-Man’ or square) and the background (texture or uniform) was varied. Please note that these videos are short sample segments from the experiment, and that in the actual experiment the rest blocks surrounding the stimulus presentations were much longer. The stimulus design of the main experiment is adapted from Akin et al. (2014). Akin, B., Ozdem, C., Eroglu, S., Keskin, D. T., Fang, F., Doerschner, K., Kersten, D., Boyaci, H. (2014). Attention modulates neuronal correlates of interhemispheric integration and global motion perception. Journal of Vision, 14(12). https://doi.org/10.1167/14.12.30 {"references": ["Akin, B., Ozdem, C., Eroglu, S., Keskin, D. T., Fang, F., Doerschner, K., Kersten, D., Boyaci, H. (2014). Attention modulates neuronal correlates of interhemispheric integration and global motion perception. Journal of Vision, 14(12). https://doi.org/10.1167/14.12.30"]}

What is selected when attention is directed to a specific location of the visual field? Theories of object-based attention have suggested that when spatial attention is directed to part of an object, attention does not simply enhance the attended location but automatically spreads to enhance all locations that comprise the object. Here, we tested this hypothesis by reconstructing the distribution of attention from V1 population neuronal activity patterns in twenty-four human adults (17 female) using functional magnetic resonance imaging (fMRI) and population-based receptive field mapping. We find that attention spreads from a spatially cued location to the underlying object – and enhances all spatial locations that comprise the object. Importantly, this spreading was also evident when the object was not task-relevant. These data suggest that attentional selection automatically operates at an object level, facilitating the reconstruction of coherent objects from fragmented representations in early visual cortex.

This is a collection of mouse resting-state fMRI datasets collected by Dr. J. Grandjean in two laboratories (ETH Zurich, Singapore Bioimaging Consortium). The datasets were processed using a common pipeline (see Associated analysis tools). The datasets contain both control animals and experimental animals (transgenic models for Alzheimer's disease, chronic stress model for depression). data/ contains preprocessed NIFTI into common space diagnostic/ contains QA summary motion/ contains motion parameters template/ contains the AIBS template and mask resampled at 200um timeseries/ contains time series extracted using an AIBS-derived atlas atlas.tsv and .json contain the atlas region-of-interest list and description participants.tsv and .json contain the study participants list and description

This thesis is divided into two parts. The first part addresses synchronisation between the rate of frequency the MR system used for fMRI examinations at Haukeland universitetssjukehus operates on (10 Mhz) and the sampling rate (5 kHz) of the EEG equipment used for audiovisual tasks. fMRI provides good spatial resolution, but relatively low time resolution. EEG has a better time resolution, but low spatial resolution. The combination of EEG and fMRI data collection will provide a good picture of dynamic processes in the brain in space and time. A simple clock divider programmed on an FPGA converts the clock signal from the MR (10 MHz), to a stable 5 kHz clock signal synchronised with the MR clock signal. The secon part of this thesis covers external referencing for the quantification of MRS data. Abolute measurements of in-vivo metabolite levels in the human brain lack a stable reference for signal intensity. A suggested solution is to introduce an external signal to provide a stable reference point for further analysis. Two systems were developed, a simple electrical system with a small loop antenna coupled to a signal generator, and an optical system. Several tests were performed proving that the optical system is more stable and safe than the electrical system. Several tests was performed on the optical system to prove that the user has full control of the position of the signal peak in the MRS spectrum, both in frequency and amplitude. The results show that there are part large variations in the quantitative measurements, and this is explained by the orientation of the antenna in relations to the MR system due to the current antenna having stronger electromagnetic radiation in different directions in space. Denne oppgaven er todelt. Første del tar for seg synkronisering mellom frekvensraten som MR-systemet brukt til fMRI undersøkelser ved Haukeland universitetssjukehus opererer på (10 MHz) og samplingsraten til EEG-utstyret (5 kHz) som blir brukt til audiovisuelle oppgaver. Siden fMRI gir god oppløsning i rommet, men har en relativt dårlig tidsoppløsning og EEG har en bedre tidsoppløsning, men dårlig romoppløsning, vil kombinasjonen av EEG og fMRI for samtidig datainnsamling gi et godt bilde av dynamiske prosesser i hjernen i både rom og tid. En enkel klokkedeler programmert på en FPGA, konverterer klokkesignalet fra MR-maskinen på 10 MHz til et stabilt 5 kHz klokkesignal som er synkronisert med MR-maskinens klokkesignal. Den andre delen av oppgaven tar for seg ekstern referanse for kvantifisering av MRS data. Absolutte målinger av in-vivo metabolittnivåer i menneskehjernen mangler en stabil referanse for signalintensitet. En foreslått løsning er å introdusere et eksternt signal for å gi et stabilt referansepunkt for videre analyser. To systemer ble utviklet, et enkelt elektrisk system med en liten loop-antenne koblet til en signalgenerator, etterfulgt av et optisk system. Flere tester ble utført som beviste at det optiske systemet er mer stabilt og sikkert enn det elektriske. Flere tester på det optiske systemet ble gjort for å bevise at brukeren har full kontroll på plasseringen av signaltoppen i MRS-spekteret både i frekvens og amplitude. Resultatene viser at det er dels store variasjoner i de kvantitative målingene og dette forklares med orienteringen av antennen i forhold til MR-systemet som skyldes at den aktuelle antennen har sterkere elektromagnetisk stråling i ulike retninger i rommet. Masteroppgave i fysikk PHYS399

This upload contains the same data as published in our previous zenodo dataset upload. Unlike our previous upload, this version contains data after transferring the DICOMs directly from the Siemens Skyra 3T to our Linux machine (as done in real-time experiments). The purpose of this separate upload is to serve as sample data for our real-time cloud software, for a specific sample project. The brain data are contributed by author S.A.N. and are authorized for non-anonymized distribution.

21st year