diff --git a/content/en/project/sleepy_group/.Rhistory b/content/en/project/sleepy_group/.Rhistory new file mode 100644 index 00000000..e69de29b diff --git a/content/en/project/sleepy_group/LICENSE b/content/en/project/sleepy_group/LICENSE new file mode 100644 index 00000000..0e259d42 --- /dev/null +++ b/content/en/project/sleepy_group/LICENSE @@ -0,0 +1,121 @@ +Creative Commons Legal Code + +CC0 1.0 Universal + + CREATIVE COMMONS CORPORATION IS NOT A LAW FIRM AND DOES NOT PROVIDE + LEGAL SERVICES. DISTRIBUTION OF THIS DOCUMENT DOES NOT CREATE AN + ATTORNEY-CLIENT RELATIONSHIP. CREATIVE COMMONS PROVIDES THIS + INFORMATION ON AN "AS-IS" BASIS. CREATIVE COMMONS MAKES NO WARRANTIES + REGARDING THE USE OF THIS DOCUMENT OR THE INFORMATION OR WORKS + PROVIDED HEREUNDER, AND DISCLAIMS LIABILITY FOR DAMAGES RESULTING FROM + THE USE OF THIS DOCUMENT OR THE INFORMATION OR WORKS PROVIDED + HEREUNDER. + +Statement of Purpose + +The laws of most jurisdictions throughout the world automatically confer +exclusive Copyright and Related Rights (defined below) upon the creator +and subsequent owner(s) (each and all, an "owner") of an original work of +authorship and/or a database (each, a "Work"). + +Certain owners wish to permanently relinquish those rights to a Work for +the purpose of contributing to a commons of creative, cultural and +scientific works ("Commons") that the public can reliably and without fear +of later claims of infringement build upon, modify, incorporate in other +works, reuse and redistribute as freely as possible in any form whatsoever +and for any purposes, including without limitation commercial purposes. +These owners may contribute to the Commons to promote the ideal of a free +culture and the further production of creative, cultural and scientific +works, or to gain reputation or greater distribution for their Work in +part through the use and efforts of others. + +For these and/or other purposes and motivations, and without any +expectation of additional consideration or compensation, the person +associating CC0 with a Work (the "Affirmer"), to the extent that he or she +is an owner of Copyright and Related Rights in the Work, voluntarily +elects to apply CC0 to the Work and publicly distribute the Work under its +terms, with knowledge of his or her Copyright and Related Rights in the +Work and the meaning and intended legal effect of CC0 on those rights. + +1. Copyright and Related Rights. A Work made available under CC0 may be +protected by copyright and related or neighboring rights ("Copyright and +Related Rights"). Copyright and Related Rights include, but are not +limited to, the following: + + i. the right to reproduce, adapt, distribute, perform, display, + communicate, and translate a Work; + ii. moral rights retained by the original author(s) and/or performer(s); +iii. publicity and privacy rights pertaining to a person's image or + likeness depicted in a Work; + iv. rights protecting against unfair competition in regards to a Work, + subject to the limitations in paragraph 4(a), below; + v. rights protecting the extraction, dissemination, use and reuse of data + in a Work; + vi. database rights (such as those arising under Directive 96/9/EC of the + European Parliament and of the Council of 11 March 1996 on the legal + protection of databases, and under any national implementation + thereof, including any amended or successor version of such + directive); and +vii. other similar, equivalent or corresponding rights throughout the + world based on applicable law or treaty, and any national + implementations thereof. + +2. Waiver. To the greatest extent permitted by, but not in contravention +of, applicable law, Affirmer hereby overtly, fully, permanently, +irrevocably and unconditionally waives, abandons, and surrenders all of +Affirmer's Copyright and Related Rights and associated claims and causes +of action, whether now known or unknown (including existing as well as +future claims and causes of action), in the Work (i) in all territories +worldwide, (ii) for the maximum duration provided by applicable law or +treaty (including future time extensions), (iii) in any current or future +medium and for any number of copies, and (iv) for any purpose whatsoever, +including without limitation commercial, advertising or promotional +purposes (the "Waiver"). Affirmer makes the Waiver for the benefit of each +member of the public at large and to the detriment of Affirmer's heirs and +successors, fully intending that such Waiver shall not be subject to +revocation, rescission, cancellation, termination, or any other legal or +equitable action to disrupt the quiet enjoyment of the Work by the public +as contemplated by Affirmer's express Statement of Purpose. + +3. Public License Fallback. Should any part of the Waiver for any reason +be judged legally invalid or ineffective under applicable law, then the +Waiver shall be preserved to the maximum extent permitted taking into +account Affirmer's express Statement of Purpose. In addition, to the +extent the Waiver is so judged Affirmer hereby grants to each affected +person a royalty-free, non transferable, non sublicensable, non exclusive, +irrevocable and unconditional license to exercise Affirmer's Copyright and +Related Rights in the Work (i) in all territories worldwide, (ii) for the +maximum duration provided by applicable law or treaty (including future +time extensions), (iii) in any current or future medium and for any number +of copies, and (iv) for any purpose whatsoever, including without +limitation commercial, advertising or promotional purposes (the +"License"). The License shall be deemed effective as of the date CC0 was +applied by Affirmer to the Work. Should any part of the License for any +reason be judged legally invalid or ineffective under applicable law, such +partial invalidity or ineffectiveness shall not invalidate the remainder +of the License, and in such case Affirmer hereby affirms that he or she +will not (i) exercise any of his or her remaining Copyright and Related +Rights in the Work or (ii) assert any associated claims and causes of +action with respect to the Work, in either case contrary to Affirmer's +express Statement of Purpose. + +4. Limitations and Disclaimers. + + a. No trademark or patent rights held by Affirmer are waived, abandoned, + surrendered, licensed or otherwise affected by this document. + b. Affirmer offers the Work as-is and makes no representations or + warranties of any kind concerning the Work, express, implied, + statutory or otherwise, including without limitation warranties of + title, merchantability, fitness for a particular purpose, non + infringement, or the absence of latent or other defects, accuracy, or + the present or absence of errors, whether or not discoverable, all to + the greatest extent permissible under applicable law. + c. Affirmer disclaims responsibility for clearing rights of other persons + that may apply to the Work or any use thereof, including without + limitation any person's Copyright and Related Rights in the Work. + Further, Affirmer disclaims responsibility for obtaining any necessary + consents, permissions or other rights required for any use of the + Work. + d. Affirmer understands and acknowledges that Creative Commons is not a + party to this document and has no duty or obligation with respect to + this CC0 or use of the Work. diff --git a/content/en/project/sleepy_group/index.md b/content/en/project/sleepy_group/index.md new file mode 100644 index 00000000..dad8c260 --- /dev/null +++ b/content/en/project/sleepy_group/index.md @@ -0,0 +1,89 @@ +--- +type: "project" # DON'T TOUCH THIS ! :) +date: "2026-06-19" # Date you first upload your project. +# Title of your project (we like creative title) +title: "Understanding Sleep vs Wake Brain Connectivity Using Simultaneous fMRI and EEG" + +# List the names of the collaborators within the [ ]. If alone, simple put your name within [] +names: [Grace Burns, Alena Ionova, Gaithtry Rameswaran, Talia Fiaani] + +# Your project GitHub repository URL +github_repo: https://github.com/brainhack-school2026/sleep_group_project + +# If you are working on a project that has website, indicate the full url including "https://" below or leave it empty. +website: + +# List +- 4 keywords that best describe your project within []. Note that the project summary also involves a number of key words. Those are listed on top of the [github repository](https://github.com/PSY6983-2021/project_template), click `manage topics`. +# Please only lowercase letters +tags: [project, github, multimodal, brainhack, fMRI, EEG, Sleep] + +# Summarize your project in < ~75 words. This description will appear at the top of your page and on the list page with other projects.. + +summary: This project investigates how resting-state functional connectivity differs between sleep and wake states using simultaneous EEG and fMRI data from the OpenNeuro "Simultaneous EEG and fMRI signals during sleep from humans" dataset. By comparing default mode network connectivity and EEG frequency-band connectivity across states, the project found minimal differences at the network level but a reliable increase in theta-band connectivity during sleep, highlighting the value of combining modalities to characterize state-dependent brain connectivity. + +# If you want to add a cover image (listpage and image in the right), add it to your directory and indicate the name +# below with the extension. +image: "sleeping_eeg_signal.jpg" +--- + + +## Project definition + +### Background + +Functional connectivity in the brain is how different regions of the brain synchronously activate to perform certain tasks. Resting State Functional Connectivity (RSFC) is a measure often used in neuroscience research to characterize this brain connectivity at rest, which can be useful in understanding which regions are communicating with each other, and if there are any disturbances to these connections. +Traditionally, RSFC is measured during an awake but relaxed state, however, this may not always be possible in certain populations like young children and is therefore sometimes done during sleep. +In this project we investigate how RSFC differs between asleep and awake states using both electroencephalography (EEG) and functional Magnetic Resonance Imaging (fMRI), two common neuroimaging modalities. +Both tools give us an understanding of brain function, but through different modalities. EEG measures the electrical activity of the brain, while fMRI measures brain activity indirectly through the Blood-Oxygen-Level-Dependent (BOLD) signal, which measures oxygenated and deoxygenated blood in different regions of the brain. + +Sleep stages are reflected in distinct EEG frequency patterns, so EEG helps identify whether the brain is in a wake-like, NREM-like, or transitional state, something fMRI alone cannot distinguish. +Subjects do commonly fall asleep during resting-state fMRI scans, likely due to the lack of stimulation and task demands (Tagliazucchi and Laufs, 2014), which has motivated the use of simultaneous EEG or eye-tracking alongside fMRI. +As EEG is sensitive to sleep stage in a way that fMRI is not, combining both modalities will allow us to more confidently characterize brain states and ask whether connectivity patterns measured with fMRI are mirrored in the EEG signals. + +### Tools + +For this project, fMRI data were analyzed using FSL and Nilearn in Python, while EEG processing and analysis were carried out using MATLAB with EEGLAB/AMRI toolboxes and MNE-Python. Jupyter notebooks were used to organize and run the analysis pipelines, with GitHub used for code sharing and version control. Together, these tools allowed us to preprocess multimodal data, calculate EEG frequency and connectivity measures, and compare brain network patterns across sleep and wake states. + +### Data + +The OpenNeuro dataset “Simultaneous EEG and fMRI signals during sleep from humans” is an open-access multimodal sleep dataset collected from 33 healthy young adults (mean ages 22.1; 17 male/ 16 female) at Pennsylvania State University. Participants completed two resting-state scans and several sleep sessions, with simultaneous EEG, fMRI, and structural MRI data collected during different brain states. The dataset also includes EEG sleep staging performed by a registered polysomnographic technologist, making it useful for comparing brain connectivity during wake/rest and sleep states (classifying epochs as wake, N1, N2 or N3). The fMRI data was already preprocessed. OpenNeuro link to access data: https://openneuro.org/datasets/ds003768/versions/1.0.13 + +### Deliverables + +At the end of this project, we created: + - Preprocessed EEG data from all 33 participants including removal of MRI interference and movement correction. + - Github repository containing the full code analysis and scripts including preprocessing and connectivity analysis. + - A results breakdown including network comparison (group level). + - Connectivity matrices (group level and individual level). + - Frequency connectivity matrices (group level). + +## Results + +### Progress overview + +Over the four weeks, we developed and ran an analysis pipeline comparing sleep and wake resting-state connectivity using fMRI and EEG. + +### Tools we learned and used during this project + + * **Terminal:** running code in the terminal + * **Python:** all scripts are written in python + * **Jupyter notebook:** all scripts were prototyped/ run in jupyter notebook + * **Git and GitHub:** for version control and open access + * **fMRI specific tools used:** FSL, NiLearn (python) + * **EEG specific tools used:** MatLab - EEGLab/ AMRI Toolboxes, MNE python + +### Results + +#### Deliverable 1: GitHub Repository + +The GitHub repository contains the full code analysis and scripts used for preprocessing, connectivity analysis, and results generation, including the network comparison, connectivity matrices, and frequency connectivity matrices described above [here](https://github.com/brainhack-school2026/sleep_group_project) . + +#### Deliverable 2: Final Presentation + +You can check out our consolidated results explained in our [final presentation slide deck](https://docs.google.com/presentation/d/1MpFA_dsS9CCAzxvj50GzfHXu-GUe8yn-H_Zna1hJcV8/edit?usp=sharing) + +## Conclusion and acknowledgement + +This project achieved a full analysis of both fMRI and EEG data, comparing connectivity between sleep and wake states. While fMRI network-level comparisons showed no significant differences between states, EEG frequency-band analysis revealed that theta-band connectivity was reliably higher during sleep than during wake, as well as higher than sleep delta and beta rhythms. + +Thank you to the BrainHack School organizers and Toronto mentors, Dr. Erin Dickie, and TAs for their guidance throughout the course. diff --git a/content/en/project/sleepy_group/sleeping_eeg_signal.jpg b/content/en/project/sleepy_group/sleeping_eeg_signal.jpg new file mode 100644 index 00000000..2c4c853a Binary files /dev/null and b/content/en/project/sleepy_group/sleeping_eeg_signal.jpg differ