Projects
Projects
Projects
Tools for Open and Reproducible Neuroscience
One of the key aspects for transparent and reproducible research is an overarching and unifying data structure which has rich metadata describing different aspects of the acquisition and experiment. The most established data structure aiming at fulfilling the role of an overarching structural organization of neuroimaging datasets is the Brain Imaging Data Structure (BIDS). BIDS is a community driven and open source effort which is constantly evolving to best fit the needs of a broad range of researchers originating from different fields within the neuroimaging domain.
Using such data structure facilitates collaborative research since there is no need to explain the data due to its commonly known structural organization. Moreover it eases the sharing of data and allows for meta analyses and big data approaches, which are referred to as gold-standard scientific practices. Since data organization is such an important and fundamental topic within the open science community our projects are centered around BIDS.
- ancpBIDS: ancpBIDS is a lightweight python library to read/query/validate/write BIDS datasets. It provides a unified and modality agnostic I/O interface for researchers to handle BIDS datasets in their workflows or analysis pipelines. Its implementation is based on the BIDS schema and allows to evolve with the BIDS specification in a generic way. For more detailed information about that library and for those who want to contribute to this open-source project check out the GitHub: ancpBIDS.
- BIDS Conversion GUI: We are currently developing an app with the purpose of converting all the data acquired at the devices in our unit (see above) into the BIDS standart. The app is implemented as a user-friendly GUI performing the conversion with minimal user input. Moreover we are currently working on the integration of new data into already existing project directories such that projects which have stopped for some reason, e.g. researchers leaving the university, can easily be continued by other researchers.
- MEGqc: Neuroimaging data is prone to many sources of noise or artifacts. That being said it seems logical that one should assess the quality of the data before analyzing them to not run into problems during the analysis because of poor data quality. Mriqc is a tool to automatically assess the quality of MRI data. The MEG community however lacks such software. For this reason we are currently developing a quality control tool in the domain of MEG. As is the case for mriqc, this tool will be based on BIDS and perform automated quality assessment given a BIDS conform MEG data set.
Brain Machine Interfacing
In a collaboration with Fraunhofer in Magdeburg, the Knight Lab at UC Berkeley and UC San Francisco we recently started a project on Brain Machine Interfacing (BMI). Our goals are to use non-invasive and invasive brain activation to control robotic devices, and for cognitive BMIs. We have recently organized the interdisciplinary 1st Magdeburg Workshop an Brain Machine Interfacing.
Publications on BMI
Collaborators: Robert T. Knight, Ulrich Schmucker, Edward Chang
Read what Bob has to say about the Newtown school shooting
Acquisition of information from natural scenes
The human visual system acquires information from cluttered natural scenes much faster and more efficient than one might expected from experiments using relatively simple stimuli (dots, gratings etc.). Only 40 ms cortical processing of a photography of a natural scene are sufficient to discriminate scenes according to their semantic content, for semantic object contetxt interactions to develop and to obtain enough information to rember the seen as previously seen. We investigate the dynamics of the information acquisition from natural scenes and the interactions between object and context at several cognitive and perceptual levels. In our investigations we combine fMRI, MEG, EEG, psychophysics, and single trial classification approaches to analyze the sequence of the brain processes involved in information extraction and recognition, the role of prior knowledge about the structure of the natural world, and to test the predictivity of brain processes for the subjective percept on a trial-by-trial basis.
Publications on natural scenes
Collaborators: Karl Gegenfurtner, Rudolf Kruse, H.H. Bülthoff
Constructive perception and eye movements:
We perceive objects in our environment as integrated wholes, even when they are covered by other objects, and thus only some fragments of the object are simulatneously visible. These subjective object percepts are of high ecological importance as they allows us to recognize and react to obects even when they are only partly visible (e.g. a predator sneaking behind trees). How the visual system constructs the subjective object percepts is still a mystery. Suggestions range from the highly cognitive "knowing what it is hypothesis" to the sensory, so-called "retinal painting hypothesis" which was put forward for example by Helmholtz some 150 years ago. The latter assumes that the eyes follow the occluded "object" and thereby paint successively visible object parts onto adjacent parts of the retina. Our investigations show that under natural free viewing conditions the retinal painting hypothsis can be rejected because retinal painting by smooth pursuit eye movements is neither necessary nor sufficient to explain the figure percept. We currently investigate the brain networks that construct the object percepts and how the brain switches between the percept of the physical stimulus and the subjective object percept.
Publications on constructive object perception and eye movements.
Collaborator: Robert Fendrich
Voluntary eye movements
Humans scan the visual environment with a rapid sequence of voluntary saccadic eye movements that move the center of regard between differnt point of interest in a scene. Despite the shifts of the retinal image we do not perceive the world as moving between saccades. This is, however, the case when the retinal images are presented as a movies. Our aim in this project was to investigate the effects of voluntary eye movements in the visual system and how the brain constructs the stable percept of the world.
Publications on constructive object perception and eye movements.
Collaborator: Ivan Bodis-Wollner
Color and motion processing
According to the classic view the brain processes visual information in a fast color insensitive and in a slow color sensitive channel.
We investigate via parametric designs using fMRI the temporal and chromatic sensitivity of visual ares in the brain with simple and complex stimuli. We implemented retinotopic mapping and other functional localizers to perform detailed measurements in independently localized visual areas.
Publications on color coding
Collaborators: Karl Gegenfurtner, Brian Wandell
Consciousness and the freedom of will
I'm interested in interdisciplinary, epistemological, and ethical aspects of the discussion about consciousness and freedom of will. Together with colleagues from Philosophy and Psychology we organized in 2002 an interdisciplinary workshop on the topic. The results are published as a book (sorry in German only).
Publications on consciousness
Collaborators: Christoph Herrmann, Silke Schicktanz, and Michael Pauen