The Stockholm Sleepy Brain Study: Effects of Sleep Deprivation on Cognitive and Emotional Processing in Young and Old

# The Stockholm SleepyBrain Project #

## Background and Aim ##

Sleepiness is a brain state with pervasive effects on cognitive and
affective functioning. However, little is known about the functional
mechanisms and correlates of sleepiness in the awake brain. This project
aimed to investigate overall effects of sleepiness on brain function
with particular regard to emotional processing.

## Method and Design ##

We investigated the effects of sleep deprivation using a randomized
cross-over design. Resting state functional connectivity was
investigated using functional magnetic resonance imaging (fMRI).
Emotional contagion was studied using concurrent fMRI and
electromyography (EMG) of facial muscles in response to emotional
expressions and empathy for pain was investigated using pictures
of others receiving pain stimuli. To study emotional reappraisal,
participants were instructed to actively up-regulate or
down-regulate their emotional responses to picture stimuli.
The participants were characterized using several rating scales,
biometric information, and blood sampling.

## Specific Notes ##

### participants.tsv File ###
Subject ID list and subject-level variables. Please refer to the
participants.json for guidance on how to interpret specific
columns in the participants.tsv file.

### BIDS dataset ###
Data were converted from DICOM source files using dcm2niix. The
parameters were further extracted from the DICOM files using pydicom
and converted to .json format. SeriesDates were anonymized and
shifted to pre-1900's years and a subject-based offset added to
the month/year that preserves time difference between initial
and follow-up visit.

T1- and T2-anatomical scans (anat/*_T{1,2}w.nii.gz) were defaced using
the pydeface.py software:
https://github.com/poldracklab/pydeface (c1ceeb2)

### derivatives Folder ###
This folder contains the processed output from the MRIQC protocol.
MRIQC is an automated processing pipeline designed to compute many
image quality metrics for T1 weighted anatomical and T2* weighted
functional scans. For more information please see:

https://github.com/poldracklab/mriqc (a5f68f5)

Additional derivatives include:

- Plots of the fMRI event logs
- thumbnail mosaics of the high-resolution T1w and T2w scans used
to confirm defacing process.

### sourcedata Folder ###
This folder contains the as-provided source files used to create the
BIDS dataset files. The only changes made to these source files were
to remove any information that could potentially be used to identify
the study participants. Specifically:

- EyeTrackingLogFiles: Files renamed, "TimeValues" and "TimeStamp"
entries changed to "REMOVED" within each file.
- PresentationLogFiles: Files renamed, scrubbed of Dates, Subject
IDs. These files were used to create the
sub-9XXX_ses-{1,2}_task-<taskname>_events.tsv
files.
- PulseGatingFiles: Files renamed to remove original IDs.
- WorkingMemoryTestResults: Files renamed to remove original IDs.,
subject IDs altered to 9XXX series randomized IDs. Dates removed.
Times-of-day left intact.

Other data that could not be included in raw form due to its binary nature:

- Physiological recordings (EMG): Converted from raw Acknowledge format
to compressed .tsv files using the "convert_physio_files.py" script
located in the code/ directory within the dataset. The output data are
located within the dataset as *_physio.tsv.gz and *_physio.json pairs.

### Diffusion Imaging - use these data with caution ###
Diffusion imaging from the following subjects should be used with
caution due to suspicious bval/bvecs tables extracted from the source
DICOM files:

sub-9019 sub-9070 sub-9057 sub-9091 sub-9090 sub-9013 sub-9044
sub-9050 sub-9067 sub-9035 sub-9035 sub-9073 sub-9083 sub-9037
sub-9007 sub-9053 sub-9066 sub-9012 sub-9082 sub-9077 sub-9076
sub-9099 sub-9001

### Raw Polysomnography Data ###
Raw polysomnography data is available upon request. Please contact Gustav Nilsonne at
[e-mail] to request this data.

### Known Issues ###
-sub-9066/ses-1/func/sub-9066_ses-1_task-hands_events.tsv does not have all of the columns present in
the other events files. It only has 'onset', 'duration' and 'condition'.

# 斯德哥尔摩嗜睡脑项目（Stockholm SleepyBrain Project）#

## 背景与研究目的 ##

嗜睡是一种对认知与情感功能具有广泛影响的脑状态。然而，目前学界对清醒状态下嗜睡的功能机制及其相关关联尚缺乏充分认知。本项目旨在探究嗜睡对脑功能的整体影响，尤其聚焦于情绪加工过程。

## 研究方法与设计 ##

本研究采用随机交叉设计，探究睡眠剥夺的影响。通过功能磁共振成像（functional magnetic resonance imaging, fMRI）考察静息态功能连接。针对情绪传染，我们采用同步fMRI与面部肌电图（electromyography, EMG）记录被试对情绪表情的反应；针对疼痛共情，则通过呈现他人接受疼痛刺激的图片开展研究。为探究情绪重评过程，要求被试主动上调或下调其对图片刺激的情绪反应。此外，通过多种评定量表、生物特征信息及血液采样对被试进行特征化表征。

## 专项说明 ##

### participants.tsv 文件 ###
该文件包含被试ID列表及被试水平变量。请参考participants.json文件，以了解如何解读participants.tsv文件中的各列信息。

### BIDS 数据集 ###
本数据集的原始数据源自DICOM文件，通过dcm2niix工具完成格式转换。进一步通过pydicom从DICOM文件中提取参数，并转换为.json格式。序列日期（SeriesDates）已进行匿名化处理：将年份调整至1900年以前，并为每位被试添加基于个体的偏移量到月份/年份中，以保留初始随访与后续随访之间的时间差。
T1及T2结构像（anat/*_T{1,2}w.nii.gz）已通过pydeface.py软件完成人脸脱敏处理：https://github.com/poldracklab/pydeface (c1ceeb2)

### 衍生数据文件夹（derivatives） ###
该文件夹包含MRIQC协议处理后的输出结果。MRIQC是一款自动化处理流程工具，用于计算T1加权结构像及T2*加权功能像的多项图像质量指标。更多信息请参阅：https://github.com/poldracklab/mriqc (a5f68f5)
额外衍生数据包括：
- fMRI事件日志绘图
- 高分辨率T1w及T2w扫描的缩略图拼接图，用于验证人脸脱敏流程。

### 源数据文件夹（sourcedata） ###
该文件夹包含用于生成BIDS数据集文件的原始源文件。对这些源文件仅进行了一项修改：移除所有可能用于识别研究被试的信息。具体修改如下：
- 眼动日志文件（EyeTrackingLogFiles）：文件已重命名，每个文件中的"TimeValues"与"TimeStamp"条目均修改为"REMOVED"。
- 刺激呈现日志文件（PresentationLogFiles）：文件已重命名，并移除了日期与被试ID信息。此类文件用于生成sub-9XXX_ses-{1,2}_task-<taskname>_events.tsv文件。
- 脉冲门控文件（PulseGatingFiles）：文件已重命名，以移除原始ID。
- 工作记忆测试结果文件：文件已重命名以移除原始ID，被试ID已替换为9XXX系列随机ID，日期信息已移除，但时刻信息予以保留。
由于部分数据为二进制格式，无法以原始形式纳入数据集，具体包括：
- 生理记录数据（EMG）：已通过数据集code/目录下的"convert_physio_files.py"脚本，从原始Acknowledge格式转换为压缩.tsv文件。输出数据以*_physio.tsv.gz与*_physio.json配对文件的形式存储于数据集内。

### 弥散成像使用提示 ###
由于从源DICOM文件中提取的bval/bvecs表存在异常，以下被试的弥散成像数据请谨慎使用：
sub-9019、sub-9070、sub-9057、sub-9091、sub-9090、sub-9013、sub-9044
sub-9050、sub-9067、sub-9035、sub-9035、sub-9073、sub-9083、sub-9037
sub-9007、sub-9053、sub-9066、sub-9012、sub-9082、sub-9077、sub-9076
sub-9099、sub-9001

### 原始多导睡眠图数据 ###
原始多导睡眠图数据可按需获取。如需获取此类数据，请联系Gustav Nilsonne，邮箱：[e-mail]。

### 已知问题 ###
sub-9066/ses-1/func/sub-9066_ses-1_task-hands_events.tsv文件缺失其他事件文件中均包含的部分列，仅包含onset、duration与condition三列。

搜集汇总

背景与挑战

背景概述

该数据集是斯德哥尔摩困倦大脑研究，旨在探究睡眠剥夺对年轻和年老个体认知和情感处理的影响。采用随机交叉设计，结合功能磁共振成像（fMRI）、肌电图（EMG）和多种任务（如情绪传染、疼痛共情、情绪重新评估），数据包括86名参与者的MRI记录，遵循BIDS格式，并附带衍生数据和注意事项，如部分扩散成像数据需谨慎使用。