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Data and codes



Intensity-based masking (IBM) tool

For our intensity-based masking tool (Peer et al. 2016, Human Brain Mapping), click here.




Functional networks in the white-matter - atlas and analysis codes

For our data and analysis codes of functional connectivity in the white-matter (Peer et al. 2017, Journal of Neuroscience), click here.




Functional connectivity in anti-NMDA receptor encephalitis - data and analysis codes

For anti-NMDA receptor encephalitis patients' and controls' data (correlation matrices) and analysis codes (Peer et al. 2017, the Lancet Psychiatry), click here.




Resting-state fMRI connectivity analysis tool

For our lab's functional connectivity analysis tool, click here.





Lab resources



fMRI

Functional magnetic resonance imaging (fMRI) is a neuroimaging technique which provides high resolution, non-invasive measures of neural activity detected by a blood oxygen level dependent (BOLD) signal. The increased blood flow to the local vasculature that accompanies neural activity in the brain results in a corresponding local reduction in deoxyhemoglobin because the increase in blood flow occurs without an increase of similar magnitude in oxygen extraction. Deoxyhemoglobin acts as an endogenous contrast enhancing agent, and serves as the source of the signal for fMRI. This technique is characterized by high spatial resolution (up to 1x1x1 mm3), but poor temporal resolution (2-3 s).


High-density EEG

Evoked potential mapping (or EP mapping) has the great advantage of measuring electrophysiological brain signals with a temporal resolution in the range of milliseconds. EP mapping is based on the examination of the global electric field at each moment in time recorded from 64 to 256 scalp electrodes. Any neuronal activity in the brain generates electric current flow. Since the brain is a volume conductor, the sum of all currents at any given moment in time is expressed by an electric potential distribution on the scalp, i.e. a momentary electric field. The electroencephalogram is basically the recording of this electric field potential at discrete scalp positions. With sufficient electrodes, the surface electric field can be reconstructed (so-called EEG/EP Mapping). Any change of the configuration of this field over time or between experimental conditions is due to a change of the active neuronal populations in the brain. EP mapping defines changes in map configuration over time and between conditions in our cognitive experiments. EEG/EP Mapping is combined with the applications of different source localization algorithms in order to localize the generators of the maps in human cortex.


Video-EEG

Patients at the department of neurology, psychiatry and neurosurgery are often simultaneously recorded by EEG and video in order to better treat epilepsy and related neuropsychiatric disorders. With their permission the recorded data may be used to better understand the neural mechanisms underlying various neuropsychiatric phenomena such as epilepsy, conversion disorders and non-epileptic seizures, dissociative disorders and more.




Intracranial EEG

Intracranial EEG (or ECOG) has the great advantage of measuring electrophysiological brain signals directly from the brain. Nowadays it is the only option oto record brain activity (in terms of LFP, local field potentials) from the behaving human. This is done mostly in the context of epilepsy surgery, while patients are evaluated and stimulated for precisely evaluated the location of the epileptic focus and its functional role. Patients are recorded continuously and may also volunteer for further cognitive paradigms during their clinical evaluation,




Direct current stimulation

Transcranial direct current stimulation (tDCS) involves applying weak electrical currents to the head, to generate an electromagnetic field which modulates the activity of neurons in specific brain parts. tDCS is known to selectively modulate neuronal excitability and can be used directly on the human cortex (in the setting of epilepsy surgery or awake craniotomy) or on the scalp. It is well known that direct stimulation prevents epileptic seizures for a while after stimulation, and extracranial stimulation is being investigated as a treatment for a variety of conditions such as depression, anxiety, and even schizophrenia. Extensive neurophysiological experiments have shown evidence that Direct Current (DC) penetrates the brain and modifies neuronal trans-membrane potentials, thereby influencing the neurons' level of excitability and modulating their firing rate.




Network analysis

Most common techniques of brain imaging attempt to find local foci of neuronal activity. However, these foci are connected and thus comprise a complex network. Tools from the field of graph theory enable us to uncover the characteristics of this brain network and to identify network and connectivity changes which occur in disease states.




Neuropsychology

Neuropsychology studies the behavioral effects of brain damage and electrical cortical stimulation on human brain functions (such as language, body knowledge, visuo-spatial cognition) and phenomenological states (illusions, hallucinations, delusions). In comparison to neuroimaging data that present correlative evidence for the implication of a given area at a given time for a certain brain function, neuropsychological data provide causal evidence for the implication of a given area for a certain brain function. Neuropsychology thus has the power to demonstrate whether a brain region is necessary for a certain function. We use classical tests such as paper and pencil type tests, computer-based stimulus presentation, and virtual reality techniques (under development). We use recording of eye movements, recording of arm and body movements in order to improve reliability and accuracy, also to making the testing more enjoyable for the patients. Neuropsychological techniques are complemented by neuroimaging techniques such as functional MRI and evoked potential mapping. For example, patients with brain injuries may take part in neuroimaging studies to investigate the effects of a lesion on the functioning of other, undamaged areas of the brain.


Psychophysics

Psychophysical methodologies are commonly used to explore the relationship between the observer's psychological states, assessed via their responses in a given task, to finely controlled manipulations of the physical stimulus. Stimuli are carefully chosen to target only the specific perceptual processes of interest. In the Laboratory, we investigate in such a way visual and audio-visual biological motion perception. Different thresholds for different stimuli can help to reveal why some stimuli are easier or harder to perceive than others. Such results can inspire new computational and neural models of perceptual processing in the brain, and further test their predictions. Psychophysical experiments can be run using only a computer and a good display and important insights into brain function can be obtained just by testing small groups of normal healthy adults. However, also here the power is enhanced if psychophysics are combined with neuroimaging techniques such as evoked potential mapping and functional MRI, to observe how the activity of specific areas in the brain is correlated with observer's performance as a function of the stimulus.


Lesion Analysis

Lesion analysis techniques have been developed to identify common brain regions involved in a particular neurological syndrome, by studying a group of patients. The neurological patients are recruited at the Department of Neurology. In order to identify the brain regions, we use two types of overlap analyses:

1. Overlap analysis after segmentation of the 'native' (non-normalized) brain images using anatomical landmarks, in collaboration with Dr L. Spinelli (Geneva University Hospital).

2. Overlap analysis after segmentation, normalization, statistical parametric mapping (SPM), and voxel-based symptom mapping, in collaboration with Dr L. Spinelli (Geneva University Hospital).



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