Page Last Updated: October 16, 2025
Structural MRI (sMRI)🔗
Release Data🔗
Structural MRI 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.
- Raw BIDS stored under subject- and session-specific
anat/folders - Derivatives generated by various pipelines
- Tabulated data derived from pipeline outputs — see the full list of tables here
Anatomical files include T1- and T2-weighted MRI images with accompanying sidecar JSONS for metadata. See BIDS Conversion Procedures.
hbcd/
|__ rawdata/
|__ sub-{ID}/
|__ ses-{V0X}/
|__ anat/
|__ sub-{ID}_ses-{V0X}_run-{X}_T1w.nii.gz
|__ sub-{ID}_ses-{V0X}_run-{X}_T1w.json
|__ sub-{ID}_ses-{V0X}_run-{X}_T2w.nii.gz
|__ sub-{ID}_ses-{V0X}_run-{X}_T2w.json
BIBSNet outputs brain segmentations and masks in native T1w and T2w space as well as volumes.tsv files with ROI volume statistics. See the pipeline documentation for a full explanation of derivatives.
hbcd/
|__ derivatives/
|__ bibsnet/
|__ sub-{ID}/
|__ ses-{V0X}/
|__ anat/
|__ sub-{ID}_ses-{V0X}_space-<T1w|T2w>_desc-aseg_dseg.nii.gz (+JSON)
|__ sub-{ID}_ses-{V0X}_space-<T1w|T2w>_desc-aseg_volumes.tsv (+JSON)
|__ sub-{ID}_ses-{V0X}_space-<T1w|T2w>_desc-aseg_brain-mask.nii.gz (+JSON)
MRIQC extracts image quality metrics (IQMs) from structural data (T1w and T2w) and also generates visual .html reports. See the pipeline documentation for a full explanation of derivatives.
hbcd/
|__ derivatives/
|__ mriqc/
|__ sub-{ID}/
| |__ ses-{V0X}/
| |__ anat/
| | |__ sub-{ID}_ses-{V0X}_run-{X}_T1w.json
| | |__ sub-{ID}_ses-{V0X}_run-{X}_T2w.json
|
|__ sub-{ID}_ses-{V0X}_run-{X}_T1w.html
|__ sub-{ID}_ses-{V0X}_run-{X}_T2w.html
See the anat/ subfolders of Infant fMRIPrep (here) and XCP-D (here) derivatives documented on the Functional MRI page, including T1w/T2w images processed to correct for motion and distortions and surface reconstructions.
Data Acquisition🔗
HBCD protocols for structural MRI were informed by recent large-scale developmental neuroimaging studies including ABCD, HCP Lifespan, and BCP (Howell et al., 2019). These studies laid critical foundation for the development of well-validated, high-resolution protocols harmonized across all three major scanner vendors (Casey et al., 2018). In addition, the findings emphasized the importance of T2w acquisition in infants due to suboptimal grey/white T1w contrast resulting from incomplete myelination (Howell et al., 2019, Myers et al., 2023).
Key features of the HBCD T1w and T2w structural imaging protocols include:
- 0.8 mm isotropic resolution
- The use of compressed SENSE reconstructions to allow high acceleration factors and thus much shorter acquisition times (under 9 minutes total for T1w and T2w – see vendor specific pages for details)
- The use of embedded navigators to track motion during structural imaging (White et al., 2010, Tisdall et al., 2016, Andersen et al., 2019). In the current release, scans were not prospectively corrected for motion, although this is intended to come online in later releases.
- As with the ABCD Study, the contrast-relevant parameters are matched as closely as possible across vendors for the T1w scans.
- Also similar to the ABCD Study, for the T2w scans, vendor-specific parameters were chosen to achieve similar contrast and SNR, accounting for the fact that each vendor implements their 3D T2w pulse sequences differently.
References🔗
Andersen, M., Björkman-Burtscher, I. M., Marsman, A., Petersen, E. T., & Boer, V. O. (2019). Improvement in diagnostic quality of structural and angiographic MRI of the brain using motion correction with interleaved, volumetric navigators. PLoS One, 14(5), e0217145. https://doi.org/10.1371/journal.pone.0217145
Casey, B. J., Cannonier, T., Conley, M. I., Cohen, A. O., Barch, D. M., Heitzeg, M. M., Soules, M. E., Teslovich, T., Dellarco, D. V., Garavan, H., Orr, C. A., Wager, T. D., Banich, M. T., Speer, N. K., Sutherland, M. T., Riedel, M. C., Dick, A. S., Bjork, J. M., Thomas, K. M., … ABCD Imaging Acquisition Workgroup. (2018). The Adolescent Brain Cognitive Development (ABCD) study: Imaging acquisition across 21 sites. Developmental Cognitive Neuroscience, 32, 43–54. https://doi.org/10.1016/j.dcn.2018.03.001
Howell, B. R., Styner, M. A., Gao, W., Yap, P.-T., Wang, L., Baluyot, K., Yacoub, E., Chen, G., Potts, T., Salzwedel, A., Li, G., Gilmore, J. H., Piven, J., Smith, J. K., Shen, D., Ugurbil, K., Zhu, H., Lin, W., & Elison, J. T. (2019). The UNC/UMN Baby Connectome Project (BCP): An overview of the study design and protocol development. NeuroImage, 185, 891–905. https://doi.org/10.1016/j.neuroimage.2018.03.049
Myers, M. J., Labonte, A. K., Gordon, E. M., Laumann, T. O., Tu, J. C., Wheelock, M. D., Nielsen, A. N., Schwarzlose, R., Camacho, M. C., Warner, B. B., Raghuraman, N., Luby, J. L., Barch, D. M., Fair, D. A., Petersen, S. E., Rogers, C. E., Smyser, C. D., & Sylvester, C. M. (2023). Functional parcellation of the neonatal brain. In bioRxivorg. https://doi.org/10.1101/2023.11.10.566629
Tisdall, M. D., Reuter, M., Qureshi, A., Buckner, R. L., Fischl, B., & van der Kouwe, A. J. W. (2016). Prospective motion correction with volumetric navigators (vNavs) reduces the bias and variance in brain morphometry induced by subject motion. Neuroimage, 127, 11-22. https://doi.org/10.1016/j.neuroimage.2015.11.054
White, N., Roddey, C., Shankaranarayanan, A., Han, E., Rettmann, D., Santos, J., Kuperman, J., & Dale, A. (2010). PROMO: Real-time prospective motion correction in MRI using image-based tracking. Magnetic Resonance in Medicine, 63(1), 91–105. https://doi.org/10.1002/mrm.22176