Page Last Updated: November 4, 2025

Overview & MR Protocols🔗

HBCD includes a suite of magnetic resonance imaging (MRI) and spectroscopy (MRS) data measures acquired as part of a comprehensive pediatric neuroimaging protocol, meticulously designed to overcome technical challenges of imaging early in life. MR data are acquired during visits V02, V03, V04, and V06 across all 27 Study recruitment sites. MR modalities include the following - click to be directed to modality documentation pages:

Release Data🔗

This data has known issues - see details.

MRI and MRS release data include both file-based (raw and processed data files in modality-specific formats) and tabulated (instrument and derived data in a standardized table format) data.
See the Data Structure Overview for a full explanation of these data types.

hbcd/
|__ rawdata/ 
|   |__ phenotype/   # Tabulated Data 
|   |   |__ img_*   
|   |
|   |__ sub-{ID}/    # Raw BIDS (file-based data)
|       |__ ses-{V0X}/ 
|           |__ anat/
|           |__ dwi/
|           |__ fmap/
|           |__ func/
|           |__ mrs/
|
|__ derivatives/     # Derivatives (file-based data) 
    |__ bibsnet/
    |__ freesurfer/
    |__ mcribs/
    |__ mriqc/
    |__ nibabies/
    |__ qmri_postproc/
    |__ qsiprep/
    |__ qsirecon/
    |__ qsirecon-*/
    |__ symri/
    |__ xcp_d/

MRI Derivatives: Quick Start Guide🔗

Below is a summary of key MRI derivatives used for structural morphology and resting-state functional MRI (rsfMRI) functional connectivity analyses. Key derivatives are produced by the XCP-D pipeline, which builds on BIBSNet and Infant-fMRIPrep outputs to produce fully preprocessed, denoised, and quality-assessed data. The full list of available XCP-D outputs are documented here. Click to expand sections below for details.

Structural Morphology: Key Derivatives for Analysis ▸

Curvature, Sulcal Depth, & Cortical Thickness

File: anat/*_space-fsLR_den-91k_<curv|sulc|thickness>.dscalar.nii
Recommended for: Vertex-wise cortical morphology analyses (e.g., folding, curvature, thickness comparisons).

These CIFTI scalar files contain surface-based structural metrics derived from reconstructed L/R cortical surfaces, aligned to the fsLR template (~64k vertices per hemisphere).

  • Curvature: Characterizes cortical folding and morphology; often used as a covariate in morphometric analyses.
  • Sulcal depth: Complements curvature to describe cortical shape and folding complexity.
  • Cortical thickness: Distance between pial and white matter surfaces (mm); typically averaged within ROIs or compared across participants to study development, aging, or group effects.

Parcellated Structural Measures

File: anat/*_space-fsLR_seg-<PARC>_stat-mean_desc-<curv|sulc|thickness>_morph.tsv
Recommended for: Region-based (ROI-level) analyses such as group comparisons or developmental modeling.

Tabulated summaries of cortical metrics (curvature, sulcal depth, thickness) within anatomical regions defined by parcellation atlases. These files provide regional averages for statistical modeling or visualization.

Midthickness, Pial, and White Matter Surfaces

File: anat/*_hemi-<L|R>_space-fsLR_den-32k_<midthickness|pial|white>.surf.gii
Recommended for: Visualizing cortical anatomy or mapping functional data to anatomical space.

3D surface models representing the midthickness, gray–white matter boundary, and pial surfaces for each hemisphere. Useful for rendering structural data, computing surface-based metrics, or visualizing functional overlays.

Functional Connectivity: Key Derivatives for Analysis ▸

Dense Timeseries

File: func/*_task-rest_space-fsLR_den-91k_desc-<denoised|denoisedSmoothed>_bold.dtseries.nii
Recommended for: Voxelwise or seed-based FC analyses, timeseries analysis via sliding windows or markov chains, etc.

CIFTI dense time series containing fully preprocessed, temporally filtered, and nuisance-regressed BOLD data. These files combine the left and right surfaces, aligned to the standard fsLR surface template, with the subcortical volume annotated by subcortical structure. Each greyordinate (~96k total) represents a vertex or voxel with pre-processed resting-state functional MRI time-series.

Parcellated Timeseries

File: func/*_task-rest_space-fsLR_seg-<PARC>_stat-mean_timeseries.tsv
Recommended for: ROI-to-ROI connectivity or network analyses using mean BOLD signals per region.

Tabulated mean BOLD time series for each region in the parcellation atlases. Also available as CIFTI .ptseries.nii files, where columns = regions and rows = timepoints.

Connectivity Matrices

File: func/*_task-rest_space-fsLR_seg-<PARC>_stat-pearsoncorrelation_relmat.tsv
Recommended for: Quick inspection, validation, or as input to network and graph analyses.

Tab-delimited matrices of pairwise Pearson correlations between atlas regions, computed from parcellated time series using all available low-motion data (motion censored with a framewise displacement threshold of 0.3 mm). These matrices form the foundation for ROI-to-ROI connectivity analyses.

Motion Detection and Confound Files

File: func/*_task-rest_dir-PA_run-{X}_<design|motion|outliers>.tsv
Required for: Motion assessment and filtering low-quality data prior to group analyses.

Includes framewise displacement values and nuisance regressor design files. Design files contain one column per regressor (e.g., motion parameters, high-motion outlier volume indicators). See the XCP-D documentation for details.

Parcellations ▸

See Parcellations & Atlases in the XCP-D documentation for more details.

Atlas Description Recommended Use
Glasser Population-level multimodal anatomical atlas (Glasser et al., 2016). Population-level structure and surface-based morphology.
Gordon 333-ROI template from rs-fMRI boundary detection for 120 young adults with 14 minutes of data collected on average (Gordon et al., 2016). Functional network mapping and group-level FC analyses.
HCP 360-ROI atlas parcellated from combining task, rest, and diffusion MRI data of 210 young adults (Glasser et al., 2013). Cross-modal structural-functional alignment.
MIDB Precision atlas derived from ABCD data, 75% probability threshold (Hermosillo et al., 2024). Individualized functional network mapping.
Myers-Labonte Infant probabilistic atlas, 50% probability threshold (Meyers et al., 2023). Infant individualized functional network mapping.
Tian Subcortical parcellation atlas (Tian et al., 2020). Subcortical connectivity analyses.
4SSchaefer Supplemented with Subcortical Structures Atlas Integrated multimodal atlas combining cortical (at ten resolutions, 100-1000 parcels), subcortical, and cerebellar structures (AtlasPack). Cross-modality alignment across XCP-D, QSIPrep, and ASLPrep outputs.

Additional Resources

HBCD Derivatives: List of MRI pipeline derivatives with links to documentation
fMRI Release Data (XCP-D): Overview of XCP-D derivatives included in the HBCD release
HBCD Processing Documentation (XCP-D): Pipeline parameters and configurations used for HBCD processing
Official XCP-D Documentation: Comprehensive documentation of all XCP-D outputs

MRI & MRS Protocols🔗

See HBCD Study MRI Protocols for full MRI protocols, sequence installation, and operation instructions.