A comprehensive clinical, MRI, and MEG collection characterizing healthy research volunteers collected at the National Institute of Mental Health (NIMH) Intramural Research Program (IRP) in Bethesda, Maryland using clinical assessments such as assays of blood and urine, mental health assessments, diagnostic and dimensional measures of mental health, cognitive and neuropsychological functioning, structural and functional magnetic resonance imaging (MRI), along with diffusion tensor imaging (DTI), and a comprehensive magnetoencephalography battery (MEG).
In addition, blood samples of healthy volunteers are banked for future genetic analyses. All data collected in this protocol are broadly shared here, in the Brain Imaging Data Structure (BIDS) format. In addition, task paradigms and basic pre-processing scripts are shared on GitHub. There are currently few open access MEG datasets, and multimodal neuroimaging datasets are even rarer. Due to its depth of characterization of a healthy population in terms of brain health, this dataset may contribute to a wide array of secondary investigations of non-clinical and clinical research questions.
This dataset is licensed under the Creative Commons Zero (CC0) v1.0 License.
This study is a convenience sample of healthy persons in the DC metropolitan area interested in participating in research. Inclusion criteria for the study require that participants are adults at or over 18 years of age in good health with the ability to read, speak, understand, and provide consent in English. All participants provided electronic informed consent for online screening and written informed consent for all other procedures. Exclusion criteria include:
- A history of significant or unstable medical or mental health condition requiring treatment
- Current self-injury, suicidal thoughts or behavior
- Current illicit drug use by history or urine drug screen
- Abnormal physical exam or laboratory result at the time of in-person assessment
- Less than an 8th grade education or IQ below 70
- Current employees, or first-degree relatives of NIMH employees, although other NIH employees may participate
Study participants are recruited through direct mailings, bulletin boards and listservs, outreach exhibits, print advertisements, and electronic media.
All potential volunteers first visit the study website (https://nimhresearchvolunteer.ctss.nih.gov), check a box indicating consent, and complete preliminary self-report screening questionnaires. The study website is HIPAA compliant and therefore does not collect Personally Identifiable Information (PII) ; instead, participants are instructed to contact the study team to provide their identity and contact information. The questionnaires include:
- Demographics
- Clinical history including medications
- Disability status (WHODAS 2.0)
- Mental health symptoms (modified DSM-5 Self-Rated Level 1 Cross-Cutting Symptom Measure)
- Substance use survey (DSM-5 Level 2)
- Alcohol use (AUDIT)
- Handedness (Edinburgh Handedness Inventory)
- Perceived health ratings
At the conclusion of the questionnaires, participants are again prompted to send an email to the study team. Survey results, supplemented by NIH medical records review (if present), are reviewed by the study team, who determines if the participant is likely eligible to participate as a healthy volunteer based on the inclusion/exclusion criteria. These participants are then scheduled for an in-person assessment. Follow-up phone screenings were also used to determine if participants were eligible for in-person screening.
At this visit, participants undergo a comprehensive clinical evaluation to determine final eligibility to be included as a healthy research volunteer. The mental health evaluation consists of a psychiatric diagnostic interview (Structured Clinical Interview for DSM-5 Disorders (SCID-5), along with self-report surveys of mood (Beck Depression Inventory-II (BD-II) and anxiety (Beck Anxiety Inventory, BAI) symptoms. An intelligence quotient (IQ) estimation is determined with the Kaufman Brief Intelligence Test, Second Edition (KBIT-2). The KBIT-2 is a brief (20-30 minute) assessment of intellectual functioning administered by a trained examiner. There are three subtests, including verbal knowledge, riddles, and matrices.
Medical evaluation includes medical history elicitation and systematic review of systems. Biological and physiological measures include vital signs (blood pressure, pulse), as well as weight, height, and BMI. Blood and urine samples are taken and a complete blood count, acute care panel, hepatic panel, thyroid stimulating hormone, viral markers (HCV, HBV, HIV), C-reactive protein, creatine kinase, urine drug screen and urine pregnancy tests are performed. Few participants have hematalogy, infectious_disease, lipid, urinalysis, and vitamin level test data included. In addition, blood samples that can be used for future genomic analysis, development of lymphoblastic cell lines or other biomarker measures are collected and banked with the NIMH Repository and Genomics Resource (Infinity BiologiX). Any future assessments on stored samples will be shared as they are available. The Family Interview for Genetic Studies (FIGS) was later added to the assessment in order to provide better pedigree information; the Adverse Childhood Events (ACEs) survey was also added to better characterize potential risk factors for psychopathology. The entirety of the in-person assessment not only collects information relevant for eligibility determination, but it also provides a comprehensive set of standardized clinical measures of volunteer health that can be used for secondary research.
Participants who were determined to be eligible for inclusion as healthy research volunteers based on the in-person assessment are given the option to consent for a magnetic resonance imaging (MRI) scan, which can serve as a baseline clinical scan to determine normative brain structure, and also as a research scan with the addition of functional sequences (resting state and diffusion tensor imaging). The MR protocol used was initially based on the ADNI-3 basic protocol, but was later modified to include portions of the ABCD protocol. Because there may be small changes in parameters from the standard ABCD/ADNI3 sequences, detailed sequence descriptions are shared in some_directory. Additional images collected with parameters inconsistent with the primary dataset are shared in the sourcedata directory with detailed .json files so that investigators can include them at their discretion.
On the same visit as the MRI scan, volunteers are administered a subset of tasks from the NIH Toolbox Cognition Battery. The four tasks include:
- Attention and executive functioning using Flanker Inhibitory Control and Attention Task.
- Executive functioning is also assessed using a Dimensional Change Card Sort Task.
- Episodic memory is evaluated using a Dimensional Change Card Sort Task.
- Working memory is evaluated using a List Sorting Working Memory Task.
An optional MEG study was added to the protocol approximately one year after the study was initiated, thus there are relatively fewer MEG recordings in comparison to the MRI dataset. All participants eligible for MRI who did not have contraindications such as implanted metal (which would reduce data quality) were offered participation in MEG. MEG studies are performed on a 275 channel CTF MEG system (CTF MEG, Coquiltam BC, Canada), using third-order gradient balancing for noise correction. All datasets were collected at a sampling rate of 1200Hz, with a quarter-Nyquist filter of 300Hz. The position of the head was localized at the beginning and end of each recording using three fiducial coils. These coils were placed 1.5 cm above the nasion, and at each ear, 1.5 cm from the tragus on a line between the tragus and the outer canthus of the eye. For 48 participants (as of 2/1/2022), photographs were taken of the three coils and used to mark the points on the T1 weighted structural MRI scan for co-registration. For the remainder of the participants (n=16 as of 2/1/2022), a Brainsight neuronavigation system (Rogue Research, Montréal, Québec, Canada) was used to coregister the MRI and fiducial localizer coils in realtime prior to MEG data acquisition.
Online and In-person behavioral and clinical measures, along with the corresponding phenotype file name, sorted first by measurement location and then by file name.
| Location | Measure | File Name |
|---|---|---|
| Online | Alcohol Use Disorders Identification Test (AUDIT) | audit |
| Demographics | demographics | |
| DSM-5 Level 2 Substance Use - Adult | drug_use | |
| Edinburgh Handedness Inventory (EHI) | ehi | |
| Health History Form | health_history_questions | |
| Perceived Health Rating - self | health_rating | |
| DSM-5 Self-Rated Level 1 Cross-Cutting Symptoms Measure – Adult (modified) | mental_health_questions | |
| World Health Organization Disability Assessment Schedule 2.0 (WHODAS 2.0) | whodas | |
| In-Person | Adverse Childhood Experiences (ACEs) | ace |
| Chemistry Panel | acute_care | |
| Beck Anxiety Inventory (BAI) | bai | |
| Beck Depression Inventory-II (BDI-II) | bdi | |
| Creatine Kinase, C-reactive Protein, TSH | blood_chemistry | |
| Complete Blood Count with Differential | cbc_with_differential | |
| Medical and mental health diagnosis, medications, physical exam, lab findings, vital signs, BMI | clinical_variable_form | |
| Family Interview for Genetic Studies (FIGS) | figs | |
| Hepatic Panel | hepatic | |
| Kaufman Brief Intelligence Test 2nd Edition (KBIT-2) and Visual Analogue of Effort Scale (VAS) | kbit2_vas | |
| MRI Variables form | mri_variables | |
| NIH Toolbox measures | nih_toolbox | |
| Viral markers (Hepatitis B, C and HIV) | other | |
| Perceived Health Rating - clinician | perceived_health_rating | |
| Research participation satisfaction survey | satisfaction | |
| Structured Clinical Interview for DSM-5 Disorders (SCID-5) | scid5 | |
| Urine drug screen and pregnancy test (if indicated) | urine_chemistry |
In many of the Clinical Measures data files, there exist some -999 and -777 values. They are described below:
-999means there was no response though a response was possible. The question may have been skipped over by the participant or the question flow.-777means there is no data available for a response. The question was not presented or asked to the participant. It appears in Edinburgh Handedness Inventory (EHI) data files.
The data were prepared using the following tools and filename mappings.
The 01_cris_clean_up.py python script contains the functions used to clean and convert the spreadsheet with clinical measures to BIDS-standard TSV files and their data dictionaries to BIDS-standard JSON files.
The 02_ctdb_clean_up.py python script contains the functions used to clean and convert the spreadsheet downloaded from CTDB (the database used by the study team) to BIDS-standard TSV files as well as their respective data dictionaries converted to BIDS-standard JSON files.
Some python functions common to both scripts were defined in rvoldefinitions.py
Data collected by the NIMH MEG Core was converted to BIDS-standard files using the MNE BIDS package. Associated notebooks: 1_mne_bids_extractor.ipynb & 2_bids_editor.ipynb. In addition, event codes and correct timings were generated with hv_process.py script, and the fiducial locations from the AFNI HEAD files were generated using the export_tags.py script.
We used dcm2bids v2.1.6 tool, a wrapper built on dcm2niix v1.0.20211006, to convert MRI DICOM files to BIDS-standard files. To preserve subject privacy, structural MRI scans are defaced using To preserve subject privacy, structural MRI scans are defaced using AFNI Refacer version 2.31 and defaced scans were checked for quality using VisualQC v0.6.1.
NOTE Release 1.0.0 of the dataset contains ASL scans but are NOT in BIDS format yet. This will be resolved in future releases.
The imaging_data_prep_scripts directory contains scripts and files used to process raw MRI and MEG data.
Below is a BIDS-compliant file/folder tree as it appears for subjects on OpenNeuro.
sub-ON<subject>
└── ses-01
├── anat
│ └── sub-ON<subject>_ses-01_acq-<desc>_[run-<index>]_<suffix>.<json|nii.gz>
├── perf
│ └── sub-ON<subject>_ses-01_asl.<json|nii.gz>
├── dwi
│ └── sub-ON<subject>_ses-01_dwi.<bvec|bval|json|nii.gz>
├── fmap
│ └── sub-ON<subject>_ses-01_acq-<desc>_<fieldmap|magnitude>.<json|nii.gz>
├── func
│ └── sub-ON<subject>_ses-01_task-<taskname>_<suffix>.<json|nii.gz>
├── meg
│ ├── sub-ON<subject>_ses-01_task-<taskname>_run-01_<meg|coordsystem>.json
│ ├── sub-ON<subject>_ses-01_task-<taskname>_run-01_<channels|events>.tsv
│ └── sub-ON<subject>_ses-01_task-<taskname>_run-01_meg.ds
│ ├── BadChannels
│ ├── bad.segments
│ ├── ClassFile.cls
│ ├── MarkerFile.mrk
│ ├── params.dsc
│ ├── processing.cfg
│ ├── sub-ON<subject>_ses-01_task-<taskname>_run-01_meg.<extension>
│ └── sub-ON<subject>_ses-01_task-<taskname>_run-01.xml
└── sub-ON<subject>_ses-01_scans.<json|tsv>Definitions:
<subject>= participant ID<taskname>= task name:airpuff,artifact,gonogo,haririhammer,movie,oddball,sternberg<desc>= placeholder for acquisition label for a given suffix<direction>=flipped,unflipped,forward,reverse<index>= run number/index<suffix>= placeholder to indicate the scan typeT1w:<desc>=MPRAGE,FSPGR,HighResHippoT2w:<desc>=CUBEFLAIR:<desc>=2dADNI2,3dCUBEfieldmap&magnitude:<desc>=bold,dwiT2starwboldmegasl
<extension>: indicates meg data files' type =acq,bak,hc,hist,infods,meg4,newds,res4,xml