No Description

Ece Boran beeea94476 Dateien hochladen nach '' 1 year ago
code_MATLAB 2313bd6f1c Dateien hochladen nach 'code_MATLAB' 1 year ago
data_NIX 13f31e2536 Dosyaları 'data_NIX' ye yükle 1 year ago
LICENSE 717834f1d9 Dateien hochladen nach '' 1 year ago
NIX_File_Structure.pdf 8f30a157c2 Dosyaları '' ye yükle 1 year ago
README.md feebbcdf0c Dateien hochladen nach '' 1 year ago
Subject_Characteristics.pdf b2a4acffbc gin commit from MacBook-Pro-Valerij.local 1 year ago
datacite.yml beeea94476 Dateien hochladen nach '' 1 year ago

README.md

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

Summary

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 monitoring 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).

We provide simultaneous recordings of intracranial EEG (iEEG) and neuronal spike times and waveforms, and metadata related to the task, subjects, sessions and electrodes in the NIX standard. We technically validated this dataset and provide here the spike sorting quality metrics and the spectra of iEEG signals.

We also provide a version of this dataset in the BIDS standard, excluding neuronal firing data, at https://openneuro.org/datasets/ds003374.

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, run the gin-shell. Log in using

gin login

You will be prompted to enter your user name and password. Change the current path to the directory for downloading the repository.

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>

To download all large files, use

gin get-content .

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 MATLAB code for loading the data and generating the publication figures. Main_Load_NIX_Data.m contains code snippets for reading NIX data and task related information. Main_Plot_Figures.m uses the functions Figure_2.m and Figure_3.m to generate figures.

Required dependencies to run the script Main_Load_NIX_Data.m:

Required dependencies to run the script Main_Plot_Figures.m:

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/Human_Amygdala_MUA_sEEG_FearVideo/.

Support

For questions on the dataset or the task, contact Johannes Sarnthein at johannes.sarnthein@usz.ch.

Related Publications and Datasets

  • 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
  • Fedele, T., Boran, E., Chirkov, V., Hilfiker, P., Grunwald, T., Stieglitz, L., Jokeit, H., Sarnthein, J., 2020. Dataset of neurons and intracranial EEG from human amygdala during aversive dynamic visual stimulation. OpenNeuro. https://doi.org/10.18112/openneuro.ds003374.v1.1.1

Licensing

Creative Commons License
This work is licensed under a Creative Commons CC0 1.0 Universal (CC0 1.0) Public Domain Dedication.

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;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 & Universität Zürich, 8091 Zurich, 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 Zurich, Switzerland;orcid.org/0000-0001-7729-4754
Grunwald,Thomas;Schweizerisches Epilepsie-Zentrum, 8008 Zurich, Switzerland Klinik für Neurologie, UniversitätsSpital Zürich, 8091 Zurich, Switzerland
Stieglitz,Lennart;Klinik für Neurochirurgie, UniversitätsSpital & Universität Zürich, 8091 Zurich, Switzerland
Jokeit,Hennric;Schweizerisches Epilepsie-Zentrum, 8008 Zurich, Switzerland Klinik für Neurologie, UniversitätsSpital Zürich, 8091 Zurich, Switzerland Neuroscience Center Zurich, 8057 Zurich, Switzerland
Sarnthein,Johannes;Klinik für Neurochirurgie, UniversitätsSpital & Universität Zürich, 8091 Zurich, Switzerland Neuroscience Center Zurich, 8057 Zurich, Switzerland;orcid.org/0000-0001-9141-381X
Description 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 monitoring 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 contains the simultaneous recording of intracranial EEG (iEEG) and neuronal spike times and waveforms, and localization information for iEEG electrodes. Subject characteristics and trial information are provided. We technically validated this dataset and provide here the spike sorting quality metrics and the spectra 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 CC0 1.0 Universal (CC0 1.0) Public Domain Dedication (https://creativecommons.org/publicdomain/zero/1.0/)
References 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 [10.1016/j.neuroimage.2020.116705] (IsSupplementTo)
Fedele, T., Boran, E., Chirkov, V., Hilfiker, P., Grunwald, T., Stieglitz, L., Jokeit, H., Sarnthein, J., 2020. Dataset of neurons and intracranial EEG from human amygdala during aversive dynamic visual stimulation. OpenNeuro. https://doi.org/10.18112/openneuro.ds003374.v1.1.1 [10.18112/openneuro.ds003374.v1.1.1] (IsVariantFormOf)
Funding Swiss National Science Foundation, SNSF 320030_156029
Mach-Gaensslen Stiftung
Stiftung für wissenschaftliche Forschung an der Universität Zürich
Forschungskredit der Universität Zürich
Russian Federation for Basic Research, RFBR 20-015-00176 A
Keywords Neuroscience
Electrophysiology
Human
Awake
Local field potential
Neuronal action potential
Spikes
Amygdala
Intracranial EEG
Cognitive task
Dynamic visual stimuli
Aversive stimuli
Epilepsy
Resource Type Dataset