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Dataset of neurons and intracranial EEG from human amygdala during aversive dynamic visual stimulation

Summary

xxx Update after changes in the manuscript We present an electrophysiological dataset collected from the amygdalae of nine subjects attending a visual dynamic stimulation of emotional aversive content. The subjects were patients affected by epilepsy who underwent preoperative invasive in the mesial temporal lobe. Subjects were presented with dynamic visual sequences of fearful faces (aversive condition), interleaved with sequences of neutral landscapes (neutral condition).

The dataset comprehends the simultaneous recording of intracranial EEG (iEEG) and neuronal spikes timestamps and waveforms, and localization information of iEEG electrode contacts. Subjects characteristics and trial information are provided. We technically validated this dataset and provide here spike sorting quality metric and the spectrum of iEEG signals. This dataset allows the investigation of amygdalar response to dynamic aversive stimuli at multiple spatial scales, from the macroscopic EEG to the neuronal firing in the human brain.

Downloading the data

Using gin

Create an account on gin and download the gin client as described here. On your computer, log in using

gin login

Clone the repository using:

gin get USZ_NCH/Human_Amygdala_MUA_sEEG_FearVideo

Large data files will not be downloaded automatically. To get them, use

gin get-content <filename>

Downloaded large files will be locked (read-only). You must unlock the files using

gin unlock <filename>

To remove the contents of a large file again, use

gin lock <filename>
gin remove-content <filename>

See here for detailed information on how to use gin.

Using git annex

Make sure git and git-annex are installed on your computer. Create an account on gin and upload your public SSH key to your gin profile. Then clone the repository using

git clone git@gin.g-node.org:/USZ_NCH/Human_Amygdala_MUA_sEEG_FearVideo.git

Large data files will not be downloaded automatically. To get them, use

git annex get <filename>

Downloaded large files will be locked (read-only). You must unlock the files using

git annex unlock <filename>

To remove the contents of a large file again, use

git annex --force lock <filename>
git annex drop <filename>

See the git annex documentation for details.

Using the web browser

Download the latest release as a zip file by clicking on Releases on the main page at https://gin.g-node.org/USZ_NCH/Human_Amygdala_MUA_sEEG_FearVideo. This zip file will contain all small (text) files only, while large data files will not be downloaded automatically and an empty placeholder will be put in their place. To get the full content of such a large file , download these files individually as needed from the web interface by clicking on them in the repository browser.

Repository structure

Main directory

Contains Subject_Characteristics.pdf which describes subjects and NIX_File_Structure.pdf which describes the structure of the nix files.

Directory code_MATLAB

Contains a MATLAB script (Load_Data_Example_Script.m) with code snippets to read data and task related information, and scripts (Figure_1.m and Figure_2.m) for the generation of the figures in the publication.

Directory data_NIX

Contains nix files for each session of the task. Each file is named with the format:
Data_Subject_<subject number>_Session_<session number>.h5

Updates

Updated versions of the data and codes will be provided at: https://gin.g-node.org/USZ_NCH/.

Support

For questions on the dataset or the task, contact Tommaso Fedele at tofedele@hse.ru. xxxWhich email to use here?

Related Publications

Fedele, T., Tzovara, A., Steiger, B., Hilfiker, P., Grunwald, T., Stieglitz, L., Jokeit, H., Sarnthein, J., 2020. The relation between neuronal firing, local field potentials and hemodynamic activity in the human amygdala in response to aversive dynamic visual stimuli. Neuroimage 213, 116705. https://doi.org/10.1016/j.neuroimage.2020.116705

Licensing

This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.

See LICENSE.txt for the full license.

datacite.yml
Title	Dataset of neurons and intracranial EEG from human amygdala during aversive dynamic visual stimulation
Authors	Fedele,Tommaso xxxJokeit not here?;Institute for Cognitive Neuroscience, National Research University Higher School of Economics, Russian Federation;orcid.org/0000-0001-7574-8062 Boran,Ece;Klinik für Neurochirurgie, UniversitätsSpital und Universität Zürich, 8091 Zürich, Switzerland;orcid.org/0000-0002-0395-7575 Chirkov,Valeri;Lomonosov Moscow State University, Russian Federation;orcid.org/0000-0003-3950-898X Hilfiker,Peter;Schweizerisches Epilepsie-Zentrum, 8008 Zürich, Switzerland;orcid.org/0000-0001-7729-4754 Grunwald,Thomas;Schweizerisches Epilepsie-Zentrum, 8008 Zürich, Switzerland Klinik für Neurologie, UniversitätsSpital Zürich, 8091 Zürich, Switzerland Stieglitz,Lennart;Klinik für Neurochirurgie, UniversitätsSpital und Universität Zürich, 8091 Zürich, Switzerland Sarnthein,Johannes;Klinik für Neurochirurgie, UniversitätsSpital und Universität Zürich, 8091 Zürich, Switzerland Zentrum für Neurowissenschaften Zürich, ETH Zürich, Zürich, Switzerland;orcid.org/0000-0001-9141-381X
Description	xxxUpdate after updates in the manuscript We present an electrophysiological dataset collected from the amygdalae of nine subjects attending a visual dynamic stimulation of emotional aversive content. The subjects were patients affected by epilepsy who underwent preoperative invasive in the mesial temporal lobe. Subjects were presented with dynamic visual sequences of fearful faces (aversive condition), interleaved with sequences of neutral landscapes (neutral condition). The dataset comprehends the simultaneous recording of intracranial EEG (iEEG) and neuronal spikes timestamps and waveforms, and localization information of iEEG electrode contacts. Subjects characteristics and trial information are provided. We technically validated this dataset and provide here spike sorting quality metric and the spectrum of iEEG signals. This dataset allows the investigation of amygdalar response to dynamic aversive stimuli at multiple spatial scales, from the macroscopic EEG to the neuronal firing in the human brain.
License	Creative Commons Attribution-ShareAlike 4.0 International Public License (https://creativecommons.org/licenses/by-sa/4.0/)
References	The relation between neuronal firing, local field potentials and hemodynamic activity in the human amygdala in response to aversive dynamic visual stimuli [] (IsPartOf)
Funding	xxx this part should be clarified after changes in the manuscript Swiss National Science Foundation, SNSF 320030_156029, 320030_188737, P300PA_174451 Vontobel Stiftung Mach-Gaensslen Stiftung Stiftung für wissenschaftliche Forschung an der Universität Zürich KIAS
Keywords	xxx These weren't changed after me, no more changes? Neuroscience Electrophysiology Human Awake Local field potential Neuronal action potential Spikes Medial temporal lobe Amygdala Intracranial EEG Cognitive task Dynamic visual stimuli Aversive stimuli Epilepsy
Resource Type	Dataset

README.md