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'.