Overview🔗

HBCD includes the following magnetic resonance imaging (MRI) and spectroscopy (MRS) data acquired as part of a comprehensive pediatric neuroimaging protocol, meticulously designed to overcome technical challenges of imaging early in life. All modalities are acquired during visits V02, V03, V04, and V06.

MRI Protocols🔗

HBCD Study MRI protocols and acquisition parameters are described in Dean et al. 2024. See the external HBCD Study MRI Protocols documentation for full protocols, sequence installation, and operation instructions.

Release Data🔗

MRI and MRS release data include the following - see Data Structure Overview for an explanation of these data types:

Raw BIDS	File-based data in modality-specific formats under subject- and session-specific rawdata/ folders
Derivatives	File-based data in modality-specific formats processed through HBCD pipelines
Tabulated Data	Questionnaires and select pipeline derivatives in HBCD-tabulated format - see Tabulated Imaging

hbcd/
├── rawdata/
│   ├── phenotype/  
│   │   # Tabulated data (forms, questionnaires, and pipeline-derived tables)
│   │   ├── mri_ra_prep           # Pre/post scan preparation
│   │   ├── img_brainswipes_*     # BrainSwipes QC
│   │   ├── img_mriqc_*           # MRIQC outputs (tabulated)
│   │   ├── img_bibsnet_*         # BIBSNet outputs (tabulated)
│   │   ├── img_xcpd_*            # XCP-D outputs (tabulated)
│   │   └── img_osprey_*          # OSPREY (MRS) outputs (tabulated)
│   │
│   └── sub-[ID]/  
│       # Raw BIDS imaging data (file-based)
│       └── ses-[V0X]/
│           ├── anat/             # Structural/qMRI + MRS localizers
│           ├── dwi/              # Diffusion MRI
│           ├── fmap/             # fMRI + qMRI fieldmaps
│           ├── func/             # Functional MRI
│           └── mrs/              # Spectroscopy
│
└── derivatives/
    # Processed pipeline outputs (file-based, modality-specific)
    │
    │ # Structural & functional pipelines
    ├── mriqc/
    ├── bme_x/
    ├── bibsnet/
    ├── nibabies/
    ├── freesurfer/
    ├── mcribs/
    ├── xcp_d/
    │   
    │ # Quantitative MRI
    ├── symri/
    ├── qmri_postproc/
    │
    │ # Diffusion MRI
    ├── qsiprep/
    ├── qsirecon/
    ├── qsirecon-DSIStudio/
    ├── qsirecon-DIPYDKI/
    ├── qsirecon-TORTOISE_model-MAPMRI/
    ├── qsirecon-TORTOISE_model-tensor/
    │
    │ # MRS
    └── osprey/

Exclusion Criteria🔗

Acquisition Criteria🔗

Acquisition specs, extracted post-BIDS conversion from JSON metadata, must fall within the ranges specified below in order to be included in the release or any downstream pipeline processing. Note that inclusion criteria are typically defined as acceptable ranges rather than fixed values due to variations between scanner types.

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)

Processed Derivatives🔗

Structural and functional MRI derivatives with an average BrainSwipes QC score < 0.5 were flagged for expert manual review; data with severe QC issues were excluded from release data. V02 sessions processed using Infant FreeSurfer (hash-2afa9081) for surface reconstruction were only partially evaluated due to generally poor quality and should not be used for analysis - see Data Warning.