# 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. T1w and FLAIR anatomical scans 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) Please note that the FLAIR images were incorrectly named with a T2w suffix at the time of the MRIQC run and thus are improperly named in the MRIQC results. This folder also contains the output from the fMRIPrep protocol. fMRIPrep is a functional magnetic resonance imaging (fMRI) data preprocessing pipeline that is designed to provide an easily accessible, state-of-the-art interface that is robust to variations in scan acquisition protocols and that requires minimal user input, while providing easily interpretable and comprehensive error and output reporting. For more information please see: https://github.com/nipreps/fmriprep Additional derivatives include: - Plots of the fMRI event logs - thumbnail mosaics of the high-resolution T1w and FLAIR scans used to confirm defacing process. - Preprocessed EMG data - Voxel displacement map generated by the FieldMap toolbox in SPM12 - Voxel-based morphometry data contributed by Dr. Zhiliang Long, please refer to https://dx.doi.org/10.1371%2Fjournal.pone.0228473 - Time-series data contributed by Dr. Govinda Poudel, please refer to the directory-level README and https://doi.org/10.1101/2020.06.04.133603 ### 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. - AdditionalSubjectLevelRatings: Item-level data for self-rated measures; genetic data; results of subjective quality inspection of T1 images. - adult_head_MRC303_Gustav_Nilsonne_20131025095652486_4.pdf: Scanning parameters - participants_extra.tsv: metadata pertaining to excluded participants - Fieldmap_RealImaginary 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 *recording-EMG_physio.tsv.gz and *recording-EMG_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 gustav.nilsonne@ki.se 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'. - sub-9070/ses-1/fmap is missing magnitude2 and phase2 files - sub-9078 has no functional images, resulting in fMRIPrep failure