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README.md

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-# Human_MTL_units_scalp_EEG_and_iEEG
-
+# Dataset of human medial temporal lobe neurons, scalp and intracranial EEG during a verbal working memory task
+
+## Summary
+We present an electrophysiological dataset recorded from nine subjects during a verbal working memory task. Subjects were epilepsy patients undergoing intracranial monitoring for localization of epileptic seizures. Subjects performed a modified Sternberg task in which the encoding of memory items, maintenance, and recall were temporally separated. The dataset includes simultaneously recorded scalp EEG with the 10-20 system, intracranial EEG (iEEG) recorded with depth electrodes, waveforms and spike times of 1526 units recorded in the medial temporal lobe, defaced MRI and CT scans, and the MNI coordinates of all intracranial electrodes. Patient characteristics and information on sessions (set size, match/mismatch, correct/incorrect, response, response time for each trial) are also provided. This dataset enables the investigation of working memory by providing simultaneous scalp EEG and iEEG recordings, which can be used for connectivity analysis, alongside hard to obtain unit recordings from humans. Moreover, the MRI and CT scans can be used to build subject-specific head models that include intracranial electrodes. Simultaneous EEG and iEEG recordings, along with the head model, can be used to validate source localization methods.
+
+## Downloading the data
+
+### Using gin
+
+Create an account on gin and download the *gin* client as described [here](https://web.gin.g-node.org/G-Node/Info/wiki/gin-cli). On your computer, log in using
+```bash
+gin login
+```
+
+Clone the repository using:
+```bash
+gin get USZ_NCH/Human_MTL_units_scalp_EEG_and_iEEG   
+```
+
+Large data files will not be downloaded automatically. To get them, use
+```bash
+gin get-content <filename>
+```
+
+Downloaded large files will be locked (read-only). You must unlock the files using
+```bash
+gin unlock <filename>
+```
+
+To remove the contents of a large file again, use
+```bash
+gin lock <filename>
+gin remove-content <filename>
+```
+
+See [here](https://web.gin.g-node.org/G-Node/Info/wiki/gin-cli+tutorial) 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
+```bash
+git clone git@gin.g-node.org:/USZ_NCH/Human_MTL_units_scalp_EEG_and_iEEG.git
+```
+
+Large data files will not be downloaded automatically. To get them, use
+```bash
+git annex get <filename>
+```
+
+Downloaded large files will be locked (read-only). You must unlock the files using
+```bash
+git annex unlock <filename>
+```
+
+To remove the contents of a large file again, use
+```bash
+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_MTL_units_scalp_EEG_and_iEEG. 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
+
+### Directory code_MATLAB
+Contains MATLAB script that contains code snippets to read data and task related information.
+
+### 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
+
+### Directory data_imaging
+Contains post implantation structural T1-weighted MRI and CT scans in the ACPC coordinate system for each subject.
+Each MRI file is named with the format: MRI\_Defaced_Subject\_\<subject number>.nii
+Each CT file is named with the format: CT\_Subject\_\<subject number>.nii
+
+## Updates
+Updated versions of the codes will be provided at:
+https://gin.g-node.org/USZ_NCH/Human_MTL_units_scalp_EEG_and_iEEG
+
+## Related Publications
+* Boran E, Fedele T, Klaver P, Hilfiker P, Stieglitz L, Grunwald T, Sarnthein J. Persistent hippocampal neural firing and hippocampal-cortical coupling predict verbal working memory load. Sci Adv 2019;5(3):eaav3687. http://doi.org/10.1126/sciadv.aav3687
+
+## Licensing
+<a rel="license" href="https://creativecommons.org/licenses/by-sa/4.0/"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by-sa/4.0/88x31.png" /></a><br />This work is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by-sa/4.0/">Creative Commons Attribution-ShareAlike 4.0 International License</a>.
+
+See `LICENSE.txt` for the full license.

datacite.yml

@@ -0,0 +1,92 @@
+# Required fields
+# The main researchers involved working on the resource,
+# or the authors of the publication in priority order.
+# May be a corporate/institutional or personal name.
+# Include digital identifier (e.g., ORCID) if possible
+authors:
+  -
+    firstname: "Ece"
+    lastname: "Boran"
+    affiliation: "Klinik für Neurochirurgie, UniversitätsSpital und Universität Zürich, 8091 Zürich, Switzerland"
+    id: "orcid.org/0000-0002-0395-7575"
+  -
+    firstname: "Tommaso"
+    lastname: "Fedele"
+    affiliation: "Klinik für Neurochirurgie, UniversitätsSpital und Universität Zürich, 8091 Zürich, Switzerland
+    Zentrum für Neurowissenschaften Zürich, ETH Zürich, Zürich, Switzerland
+    Institute for Cognitive Neuroscience, National Research University Higher School of Economics, Russian Federation"
+    id: "orcid.org/0000-0001-7574-8062"
+  -
+    firstname: "Adrian"
+    lastname: "Steiner"
+    affiliation: "Klinik für Neurochirurgie, UniversitätsSpital und Universität Zürich, 8091 Zürich, Switzerland"
+  -
+    firstname: "Peter"
+    lastname: "Hilfiker"
+    affiliation: "Schweizerisches Epilepsie-Zentrum, 8008 Zürich, Switzerland"
+    id: "orcid.org/0000-0001-7729-4754"
+  -
+    firstname: "Lennart"
+    lastname: "Stieglitz"
+    affiliation: "Klinik für Neurochirurgie, UniversitätsSpital und Universität Zürich, 8091 Zürich, Switzerland"
+  -
+    firstname: "Thomas"
+    lastname: "Grunwald"
+    affiliation: "Schweizerisches Epilepsie-Zentrum, 8008 Zürich, Switzerland
+    Klinik für Neurologie, UniversitätsSpital Zürich, 8091 Zürich, Switzerland"
+  -
+    firstname: "Johannes"
+    lastname: "Sarnthein"
+    affiliation: "Klinik für Neurochirurgie, UniversitätsSpital und Universität Zürich, 8091 Zürich, Switzerland
+    Zentrum für Neurowissenschaften Zürich, ETH Zürich, Zürich, Switzerland"
+    id: "orcid.org/0000-0001-9141-381X"
+
+# A name or title to describe the published resource.
+title: "Dataset of simultaneous scalp EEG and intracranial EEG recordings and human medial temporal lobe units during a verbal working memory task"
+
+# Any additional information. It is best practice to supply a description for the resource.
+description: |
+  We present an electrophysiological dataset recorded from nine subjects during a verbal working memory task. Subjects were epilepsy patients undergoing intracranial monitoring for localization of epileptic seizures. Subjects performed a modified Sternberg task in which the encoding of memory items, maintenance, and recall were temporally separated. The dataset includes simultaneously recorded scalp EEG with the 10-20 system, intracranial EEG (iEEG) recorded with depth electrodes, waveforms and spike times of 1526 units recorded in the medial temporal lobe, defaced MRI and CT scans, and the MNI coordinates of all intracranial electrodes. Patient characteristics and information on sessions (set size, match/mismatch, correct/incorrect, response, response time for each trial) are also provided. This dataset enables the investigation of working memory by providing simultaneous scalp EEG and iEEG recordings, which can be used for connectivity analysis, alongside hard to obtain unit recordings from humans. Moreover, the MRI and CT scans can be used to build subject-specific head models that include intracranial electrodes. Simultaneous EEG and iEEG recordings, along with the head model, can be used to validate source localization methods.
+
+# List of keywords the resource should be associated with.
+keywords:
+  - Neuroscience
+  - Electrophysiology
+  - Human
+  - Awake
+  - Local field potential
+  - Neuronal action potential
+  - Spikes
+  - Medial temporal lobe
+  - Hippocampus
+  - Entorhinal cortex
+  - Amygdala
+  - Scalp EEG
+  - Intracranial EEG
+  - Cognitive task
+  - Verbal working memory
+  - Epilepsy
+
+# Any rights information for this resource. Please provide both a license name and a link to the license.
+# Please add also a LICENSE file to the repository
+license:
+  name: "Creative Commons Attribution-ShareAlike 4.0 International Public License"
+  url: "https://creativecommons.org/licenses/by-sa/4.0/"
+
+## Optional Fields
+
+# Any funding reference for this resource. Separate funder name and grant number by comma
+funding:
+  - "Swiss National Science Foundation, SNSF 320030_176222"
+  - "Mach-Gaensslen Stiftung"
+  - "Stiftung für wissenschaftliche Forschung an der Universität Zürich"
+  - "Forschungskredit der Universität Zürich"
+
+# Related publications. reftype might be: IsCitedBy, IsSupplementTo, IsReferencedBy, IsPartOf
+# for further valid types see https://schema.datacite.org/meta/kernel-4
+# Please provide digital identifier (e.g., DOI) if possible.
+references:
+  -
+    doi: "10.1126/sciadv.aav3687"     
+    reftype: "IsPartOf"
+    name: "Persistent hippocampal neural firing and hippocampal-cortical coupling predict verbal working memory load"