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

uploaded by Ece Boran on 2020-11-11 - 12 months ago
last modified on 2020-11-26 - 11 months ago
authored by Tommaso Fedele, Ece Boran, Valeri Chirkov, Peter Hilfiker, Thomas Grunwald, Lennart Stieglitz, Hennric Jokeit, Johannes Sarnthein
104629
Your dataset is no longer valid. You must fix the 1 Error to use all of the site features.

/sub-01/ses-01/ieeg/sub-01_ses-01_space-MNI152_coordsystem.json

Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a ".bidsignore" file in your dataset (see https://github.com/bids-standard/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder.

sub-01_ses-01_space-MNI152_coordsystem.json

/sub-01/ses-01/ieeg/sub-01_ses-01_space-MNI152_electrodes.tsv

Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a ".bidsignore" file in your dataset (see https://github.com/bids-standard/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder.

sub-01_ses-01_space-MNI152_electrodes.tsv

/sub-02/ses-01/ieeg/sub-02_ses-01_space-MNI152_coordsystem.json

Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a ".bidsignore" file in your dataset (see https://github.com/bids-standard/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder.

sub-02_ses-01_space-MNI152_coordsystem.json

/sub-02/ses-01/ieeg/sub-02_ses-01_space-MNI152_electrodes.tsv

Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a ".bidsignore" file in your dataset (see https://github.com/bids-standard/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder.

sub-02_ses-01_space-MNI152_electrodes.tsv

/sub-03/ses-01/ieeg/sub-03_ses-01_space-MNI152_coordsystem.json

Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a ".bidsignore" file in your dataset (see https://github.com/bids-standard/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder.

sub-03_ses-01_space-MNI152_coordsystem.json

/sub-03/ses-01/ieeg/sub-03_ses-01_space-MNI152_electrodes.tsv

Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a ".bidsignore" file in your dataset (see https://github.com/bids-standard/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder.

sub-03_ses-01_space-MNI152_electrodes.tsv

/sub-04/ses-01/ieeg/sub-04_ses-01_space-MNI152_coordsystem.json

Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a ".bidsignore" file in your dataset (see https://github.com/bids-standard/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder.

sub-04_ses-01_space-MNI152_coordsystem.json

/sub-04/ses-01/ieeg/sub-04_ses-01_space-MNI152_electrodes.tsv

Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a ".bidsignore" file in your dataset (see https://github.com/bids-standard/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder.

sub-04_ses-01_space-MNI152_electrodes.tsv

/sub-05/ses-01/ieeg/sub-05_ses-01_space-MNI152_coordsystem.json

Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a ".bidsignore" file in your dataset (see https://github.com/bids-standard/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder.

sub-05_ses-01_space-MNI152_coordsystem.json

/sub-05/ses-01/ieeg/sub-05_ses-01_space-MNI152_electrodes.tsv

Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a ".bidsignore" file in your dataset (see https://github.com/bids-standard/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder.

sub-05_ses-01_space-MNI152_electrodes.tsv

and 8 more files

OpenNeuro Accession Number: ds003374
Files: 104, Size: 167.33MB, Subjects: 9, Session: 1
Available Tasks: jokeit
Available Modalities: iEEG

README

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 the recordings of intracranial EEG (iEEG) and metadata related to the task, subjects, sessions and electrodes in the BIDS standard.

We also provide a more extended version of the dataset that includes neuronal spike times and waveforms in the NIX standard under the folder "bidsignore/data_NIX". This extended dataset is also available in G-Node at https://gin.g-node.org/USZ_NCH/Human_Amygdala_MUA_sEEG_FearVideo/.

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.

Repository structure

Main directory

Contains metadata in the BIDS standard.

Directories sub-

Contains folders for each subject, named sub-.

Directory bidsignore

Contains data in the NIX standard, and metadata files. Subject_Characteristics.pdf describes subjects and NIX_File_Structure.pdf 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

Support

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

Authors

  • Tommaso Fedele
  • Ece Boran
  • Valeri Chirkov
  • Peter Hilfiker
  • Thomas Grunwald
  • Lennart Stieglitz
  • Hennric Jokeit
  • Johannes Sarnthein

Dataset DOI

10.18112/openneuro.ds003374.v1.1.1

License

CC0

Acknowledgements

We thank the physicians and the staff at Schweizerische Epilepsie-Klinik for their assistance and the subjects for their participation. We acknowledge grants awarded by the Swiss National Science Foundation (SNSF 320030_156029 to J.S.), Mach-Gaensslen Stiftung (to J.S.), Stiftung für wissenschaftliche Forschung an der Universität Zürich (to J.S.), Forschungskredit der Universität Zürich (to T.F.) and Russian Foundation for Basic Research (RFBR 20-015-00176 A to T.F.). The funders had no role in the design or analysis of the study.

How to Acknowledge

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

References and Links

  • 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. G-node. https://gin.g-node.org/USZ_NCH/Human_Amygdala_MUA_sEEG_FearVideo

Ethics Approvals

  • Kantonale Ethikkommission Zürich (PB-2016-02055)

How To Cite

Copy
Tommaso Fedele and Ece Boran and Valeri Chirkov and Peter Hilfiker and Thomas Grunwald and Lennart Stieglitz and Hennric Jokeit and Johannes Sarnthein (2020). Dataset of neurons and intracranial EEG from human amygdala during aversive dynamic visual stimulation. OpenNeuro. [Dataset] doi: 10.18112/openneuro.ds003374.v1.1.1
More citation info

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

uploaded by Ece Boran on 2020-11-11 - 12 months ago
last modified on 2020-11-26 - 11 months ago
authored by Tommaso Fedele, Ece Boran, Valeri Chirkov, Peter Hilfiker, Thomas Grunwald, Lennart Stieglitz, Hennric Jokeit, Johannes Sarnthein
104629

OpenNeuro Accession Number: ds003374
Files: 104, Size: 167.33MB, Subjects: 9, Session: 1
Available Tasks: jokeit
Available Modalities: iEEG

README

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 the recordings of intracranial EEG (iEEG) and metadata related to the task, subjects, sessions and electrodes in the BIDS standard.

We also provide a more extended version of the dataset that includes neuronal spike times and waveforms in the NIX standard under the folder "bidsignore/data_NIX". This extended dataset is also available in G-Node at https://gin.g-node.org/USZ_NCH/Human_Amygdala_MUA_sEEG_FearVideo/.

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.

Repository structure

Main directory

Contains metadata in the BIDS standard.

Directories sub-

Contains folders for each subject, named sub-.

Directory bidsignore

Contains data in the NIX standard, and metadata files. Subject_Characteristics.pdf describes subjects and NIX_File_Structure.pdf 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

Support

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

Authors

  • Tommaso Fedele
  • Ece Boran
  • Valeri Chirkov
  • Peter Hilfiker
  • Thomas Grunwald
  • Lennart Stieglitz
  • Hennric Jokeit
  • Johannes Sarnthein

Dataset DOI

10.18112/openneuro.ds003374.v1.1.1

License

CC0

Acknowledgements

We thank the physicians and the staff at Schweizerische Epilepsie-Klinik for their assistance and the subjects for their participation. We acknowledge grants awarded by the Swiss National Science Foundation (SNSF 320030_156029 to J.S.), Mach-Gaensslen Stiftung (to J.S.), Stiftung für wissenschaftliche Forschung an der Universität Zürich (to J.S.), Forschungskredit der Universität Zürich (to T.F.) and Russian Foundation for Basic Research (RFBR 20-015-00176 A to T.F.). The funders had no role in the design or analysis of the study.

How to Acknowledge

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

References and Links

  • 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. G-node. https://gin.g-node.org/USZ_NCH/Human_Amygdala_MUA_sEEG_FearVideo

Ethics Approvals

  • Kantonale Ethikkommission Zürich (PB-2016-02055)

How To Cite

Copy
Tommaso Fedele and Ece Boran and Valeri Chirkov and Peter Hilfiker and Thomas Grunwald and Lennart Stieglitz and Hennric Jokeit and Johannes Sarnthein (2020). Dataset of neurons and intracranial EEG from human amygdala during aversive dynamic visual stimulation. OpenNeuro. [Dataset] doi: 10.18112/openneuro.ds003374.v1.1.1
More citation info

Dataset File Tree

Git Hash: 1c85adc 

BIDS Validation

Your dataset is no longer valid. You must fix the 1 Error to use all of the site features.

/sub-01/ses-01/ieeg/sub-01_ses-01_space-MNI152_coordsystem.json

Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a ".bidsignore" file in your dataset (see https://github.com/bids-standard/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder.

sub-01_ses-01_space-MNI152_coordsystem.json

/sub-01/ses-01/ieeg/sub-01_ses-01_space-MNI152_electrodes.tsv

Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a ".bidsignore" file in your dataset (see https://github.com/bids-standard/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder.

sub-01_ses-01_space-MNI152_electrodes.tsv

/sub-02/ses-01/ieeg/sub-02_ses-01_space-MNI152_coordsystem.json

Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a ".bidsignore" file in your dataset (see https://github.com/bids-standard/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder.

sub-02_ses-01_space-MNI152_coordsystem.json

/sub-02/ses-01/ieeg/sub-02_ses-01_space-MNI152_electrodes.tsv

Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a ".bidsignore" file in your dataset (see https://github.com/bids-standard/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder.

sub-02_ses-01_space-MNI152_electrodes.tsv

/sub-03/ses-01/ieeg/sub-03_ses-01_space-MNI152_coordsystem.json

Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a ".bidsignore" file in your dataset (see https://github.com/bids-standard/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder.

sub-03_ses-01_space-MNI152_coordsystem.json

/sub-03/ses-01/ieeg/sub-03_ses-01_space-MNI152_electrodes.tsv

Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a ".bidsignore" file in your dataset (see https://github.com/bids-standard/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder.

sub-03_ses-01_space-MNI152_electrodes.tsv

/sub-04/ses-01/ieeg/sub-04_ses-01_space-MNI152_coordsystem.json

Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a ".bidsignore" file in your dataset (see https://github.com/bids-standard/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder.

sub-04_ses-01_space-MNI152_coordsystem.json

/sub-04/ses-01/ieeg/sub-04_ses-01_space-MNI152_electrodes.tsv

Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a ".bidsignore" file in your dataset (see https://github.com/bids-standard/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder.

sub-04_ses-01_space-MNI152_electrodes.tsv

/sub-05/ses-01/ieeg/sub-05_ses-01_space-MNI152_coordsystem.json

Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a ".bidsignore" file in your dataset (see https://github.com/bids-standard/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder.

sub-05_ses-01_space-MNI152_coordsystem.json

/sub-05/ses-01/ieeg/sub-05_ses-01_space-MNI152_electrodes.tsv

Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a ".bidsignore" file in your dataset (see https://github.com/bids-standard/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder.

sub-05_ses-01_space-MNI152_electrodes.tsv

and 8 more files

Dataset File Tree

Git Hash: 1c85adc 

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