Page Last Updated: October 10, 2025

File-Based Data🔗

Unlike tabulated data (tables organized in a uniform way across study instruments), file-based data comes in a variety of formats, often modality-specific. File-based data includes:

  • Raw BIDS: raw data converted to the BIDS standard with unaltered signal content
  • Derivatives: processed datasets generated by standardized pipelines

Raw BIDS🔗

See Age Variable Definitions for documentation on fields reporting age in raw BIDS data.

The rawdata/ folder includes raw file-based data in BIDS format for MRI, MRS, EEG, and wearable sensor recordings. 

hbcd/
|__ rawdata/ 
    |__ sub-{ID}/
    |   |__ sub-{ID}_sessions.tsv
    |   |__ sub-{ID}_sessions.json
    |   |__ ses-{V0X}/
    |       |__ anat/
    |       |__ dwi/
    |       |__ eeg/
    |       |__ fmap/
    |       |__ func/
    |       |__ motion/
    |       |__ mrs/
    |       |__ sub-{ID}_ses-{V0X}_scans.tsv
    |       |__ sub-{ID}_ses-{V0X}_scans.json
    |
    |__ dataset_description.json
    |__ participants.tsv
    |__ participants.json

Participant-, Session-, & Scan-Level Data🔗

Participant-, session-, and scan-level data are stored in the following .tsv files, accompanied by .json sidecar files containing metadata:

Level File Name Description
Participant participants.tsv Basic demographic and participant information (e.g., sex)
Session sub-{ID}_sessions.tsv Session information (e.g., collection site, participant’s age at each session, head size)
Scan sub-{ID}_ses-{V0X}_scans.tsv Per-scan information (age at scan and raw data QC scores - see HBCD MR Quality Control Procedures)

Modality-Specific Subfolders🔗

Click the following links to see the full file contents of each raw BIDS folder in the measure documentation pages:

Structural MRI Quantitative MRI Functional MRI Diffusion MRI MR Spectroscopy EEG Wearable Sensors
anat/ anat/ func/, fmap/ dwi/ mrs/ eeg/ motion/

BIDS Conversion Procedures🔗

Raw data for each modality are converted to the BIDS standard via the following software and procedures:

BIDS Conversion
MRI DICOM images are converted using an HBCD-customized version of dcm2niix, with post-conversion modifications required for certain scan types to maintain consistency across vendors - see MRI Hardcoded Fields & Post-Conversion Modifications below for details.
MRS Vendor-specific raw data formats (Siemens .dat; Philips data/list; GE P-file) were converted to BIDS using a wrapper (hbcd_mrs_to_nii_conversion) for spec2nii v0.7.0.
EEG BIDS conversion was performed with the EEG2BIDS Wizard, a custom MATLAB application for HBCD EEG data management and formatting, installed at all HBCD sites. After each EEG session, raw data are uploaded to the Wizard, which converts them to the BIDS standard.
Sensors See Jeung et al., 2024 Motion-BIDS: an extension to the brain imaging data structure to organize motion data for reproducible research
BIDS-logo MRI Hardcoded Fields & Post-Conversion Modifications ▸

Hardcoded Fields
Key fields for Philips (and GE for T1w scans) are hard-coded to ensure consistency across vendors, as NIfTI/JSON metadata can be omitted or misconfigured during conversion. Hardcoded fields for different modalities/scan types are outlined in the following table and also documented in the JSON sidecars under HardCodedValues. All of the following were modified for Philips only with the exception of T1w scans, modified for both Philips and GE.

Modality PhaseEncodingDirection TotalReadoutTime SliceTiming <Small|Large>Delta RepetitionTime
DWI
EPI
BOLD
T1w (both Philips & GE)

QALAS
QALAS conversion yielded either five 3D NIfTI files or one 4D file with five volumes and missing JSON headers. To standardize outputs, all series were split into five NIfTI files, each labeled by inversion time (inv-{X}). The JSON sidecars were updated as follows: T2Prep for QALAS file inv-0 is set to 0.10 for Siemens/Philips and 0.09 for GE. InversionTime (s) is hard-coded per manufacturer as follows:

inv-0inv-1inv-2inv-3inv-4
Siemens00.111.92.8
GE00.11931.01921.91912.8190
Philips00.1151.01051.90602.8016

Data Release Eligibility Criteria🔗

Acquisition parameters vary by scanner vendor, so inclusion criteria are typically defined as acceptable ranges rather than fixed values. Following BIDS conversion, modality-specific criteria are extracted from BIDS sidecar JSON files and evaluated accordingly.

Acquisition Parameter Ranges for Data Release Eligibility ▸

NOTE: All images are additionally checked to confirm they were acquired using a head coil.

Scan Type Repetition Time (TR) Echo Time (TE) Inversion Time (TI) Slice Thickness Number of Volumes
T1w 2.3 - 2.41 0.002 - 0.0035 1.06 - 1.1 0.8 NA
T2w 2.5 - 4.5 0.09 - 0.15 0.29 - 0.33 0.563 - 0.565 NA
MRS Localizer 2.5 - 4.5 0.09 - 0.15 0.29 - 0.33 0.563 - 0.565 NA
Diffusion 4.8 0.0880 - 0.0980 NA 1.7 ≥ 90 (AP + PA)
EPI Fieldmap 8.4 - 9.2 0.064 - 0.0661 2 0.563 - 0.565 NA
Functional 1.725 0.0369 - 0.0371 NA 2 ≥ 87 (~2.5 min)

Derivatives🔗

The derivatives/ folder contains derivatives, which are file outputs from processing pipelines. 

hbcd/
|__ derivatives/ 
    # Structural & Functional MRI             
    |__ mriqc/      
    |__ bibsnet/    
    |__ nibabies/   
    |__ freesurfer/ 
    |__ mcribs/     
    |__ xcp_d/      
    |               
    # Quantitative MRI    
    |__ symri/           
    |__ qmri_postproc/  
    | 
    # Diffusion MRI                                  
    |__ qsiprep/                         
    |__ qsirecon/                        
    |__ qsirecon-DIPYDKI/                
    |__ qsirecon-DSIStudio/                         
    |__ qsirecon-TORTOISE_model-MAPMRI/  
    |__ qsirecon-TORTOISE_model-tensor/  
    |
    |__ osprey/       # MRS
    |__ made/         # EEG
    |__ hbcd_motion/  # Biosensor Recordings

Modalities Derivatives Folder Pipeline Name & Link to Derivatives Link
Structural & Functional MRI mriqc/ MRIQC - sMRI & fMRI
bibsnet/ BIBSNet
nibabies/ Infant fMRIPrep (or Nibabies)
freesurfer/ & mcribs/ FreeSurfer & M-CRIB-S
xcp_d/ XCP-D
Quantitative MRI symri/ SyMRI
qmri_postproc/ qMRI PostProc
Diffusion MRI qsiprep/ QSIPrep
qsirecon/ QSIRecon
qsirecon-DSIStudio/ QSIRecon-DSI Studio
qsirecon-DIPYDKI/ QSIRecon-DIPY DKI
qsirecon-TORTOISE_model-MAPMRI/ QSIRecon-TORTOISE MAP-MRI
qsirecon-TORTOISE_model-tensor/ QSIRecon-TORTOISE Tensor
MR Spectroscopy osprey/ OSPREY-BIDS
EEG made/ HBCD-MADE
Wearable Sensors motion/ HBCD-Motion