Page Last Updated: May 17, 2026
Quantitative MRI (qMRI)🔗
Note that different sites may apply varying criteria for identifying motion-degraded QALAS and B1+ mapping scans. For 3D-QALAS, the SyMRI toolbox does not incorporate externally acquired B1+ field maps when estimating quantitative T1, T2, and proton density (PD) values.
Additionally, estimated quantitative T1 values show variability across MRI vendors and participant age. Current estimates do not align well with values reported in the literature, likely due to assumptions made in the modeling procedures. Work is ongoing to address these issues. As a result, quantitative T1 values (and by extension, PD values) will not be included initial release data.
Overview & Acquisition🔗
Conventional neuroimaging relies on qualitative relaxation-weighted images (e.g., T1w, T2w), which reflect relative differences in tissue properties, but are strongly influenced by sequence parameters, participant positioning, and scanner hardware. These dependencies limit biological interpretability and hinder comparisons across participants, sessions, and sites. The challenge is especially pronounced in pediatric imaging, where rapid age-related changes in free water distribution, iron, and myelination dynamically alter image contrast.
Quantitative MRI (qMRI) addresses these limitations by directly measuring relaxation properties, providing more reliable markers of brain tissue microstructure (Deoni 2010; Does 2018). The HBCD Study acquires 3D-QALAS, a time-efficient 3D sequence that combines interleaved Look-Locker acquisition with a T2-preparation pulse (Kvernby et al. 2014). This approach enables simultaneous estimation of T1/T2 relaxation times and proton density (PD) maps from a single scan and has been validated across major MRI vendors (Fujita et al. 2019).
QALAS
QALAS is a multi-contrast MRI sequence that produces five brain volumes using turbo-flash readouts with varying T1 and T2 weightings (acquisition time ~5 min for Siemens and ~4 min for GE/Philips). These volumes are combined to estimate T1, T2, and proton density (PD) maps. The sequence starts with a T2-preparation pulse, which adds T2 weighting to the first volume. An inversion pulse follows, imparting T1 weighting to the next four volumes.
B1+ Fieldmaps
The HBCD protocol includes a short B1+ field map acquisition (~30–45 seconds across all scanner types) to calibrate flip angle measurements, which can vary spatially due to B1+ field inhomogeneity. This calibration is required for accurate T1, T2, and PD estimation. Because the transmit B1+ field varies smoothly across space, coarse spatial resolution is sufficient, enabling rapid acquisition. Vendor-specific implementations in the HBCD protocol include Actual Flip Angle Imaging (AFI) for GE and Philips, and a pre-saturation turbo-FLASH readout for Siemens (Yarnykh 2007).
Processing & Derivatives🔗
qMRI data are processed via SyMRI followed by minimal post-processing through qMRI PostProc. SyMRI derives synthetic T1w/T2w images and quantitative relaxometry maps from 3D-QALAS acquisitions by reintroducing estimated T1/T2 relaxation times into the MR signal equation (Bloch equations).
# JSON files excluded for brevity hbcd/ └── derivatives/ │ SyMRI ├── symri/ │ └── sub-[ID]/ │ └── ses-[V0X]/ │ └── anat/ │ ├── sub-[ID]_ses-[V0X]_acq-QALAS_T1w.nii.gz │ ├── sub-[ID]_ses-[V0X]_acq-QALAS_T2w.nii.gz │ ├── sub-[ID]_ses-[V0X]_acq-QALAS_T2map.nii.gz │ └── sub-[ID]_ses-[V0X]_acq-QALAS_desc-SymriContainer.log │ qMRI PostProc └── qmri_postproc/ └── sub-[ID]/ └── ses-[V0X]/ └── anat/ ├── sub-[ID]_ses-[V0X]_desc-AsegROIs_scalarstats.tsv ├── sub-[ID]_ses-[V0X]_desc-BilateralAsegROIs_scalarstats.tsv ├── sub-[ID]_ses-[V0X]_desc-RegistrationQCAid.png ├── sub-[ID]_ses-[V0X]_space-T2w_desc-QALAS_T2map.nii.gz └── sub-[ID]_ses-[V0X]_space-QALAS_desc-aseg_dseg.nii.gz How To Read File Trees →
References🔗
Dean III, D. C., Tisdall, M. D., Wisnowski, J. L., Feczko, E., Gagoski, B., Alexander, A. L., ... & HBCD MRI Working Group. (2024). Quantifying brain development in the HEALthy Brain and Child Development (HBCD) Study: The magnetic resonance imaging and spectroscopy protocol. Developmental Cognitive Neuroscience, 70, 101452. https://doi.org/10.1016/j.dcn.2024.101452
Deoni, S. C. L. (2010). Quantitative relaxometry of the brain. Topics in Magnetic Resonance Imaging: TMRI, 21(2), 101–113. https://doi.org/10.1097/RMR.0b013e31821e56d8
Deoni, S. C. L., Rutt, B. K., & Peters, T. M. (2006). Synthetic T1-weighted brain image generation with incorporated coil intensity correction using DESPOT1. Magnetic Resonance Imaging, 24(9), 1241–1248. https://doi.org/10.1016/j.mri.2006.03.015
Does, M. D. (2018). Inferring brain tissue composition and microstructure via MR relaxometry. NeuroImage, 182, 136–148. https://doi.org/10.1016/j.neuroimage.2017.12.087
Fautz H-P, Vogel M, Gross P, Kerr A, Zhu Y. B1 mapping of coil arrays for parallel transmission. Proceedings of the 16th Annual Meeting of ISMRM, Toronto, Canada. Vol. 1247. 2008.
Fujita, S., Gagoski, B., Hwang, K.-P., Hagiwara, A., Warntjes, M., Fukunaga, I., Uchida, W., Saito, Y., Sekine, T., Tachibana, R., Muroi, T., Akatsu, T., Kasahara, A., Sato, R., Ueyama, T., Andica, C., Kamagata, K., Amemiya, S., Takao, H., … Aoki, S. (2024). Cross-vendor multiparametric mapping of the human brain using 3D-QALAS: A multicenter and multivendor study. Magnetic Resonance in Medicine, 91(5), 1863–1875. https://doi.org/10.1002/mrm.29939
Fujita, S., Hagiwara, A., Hori, M., Warntjes, M., Kamagata, K., Fukunaga, I., Andica, C., Maekawa, T., Irie, R., Takemura, M. Y., Kumamaru, K. K., Wada, A., Suzuki, M., Ozaki, Y., Abe, O., & Aoki, S. (2019). Three-dimensional high-resolution simultaneous quantitative mapping of the whole brain with 3D-QALAS: An accuracy and repeatability study. Magnetic Resonance Imaging, 63, 235–243. https://doi.org/10.1016/j.mri.2019.08.031
Gonçalves, F. G., Serai, S. D., & Zuccoli, G. (2018). Synthetic brain MRI. Topics in Magnetic Resonance Imaging: TMRI, 27(6), 387–393. https://doi.org/10.1097/rmr.0000000000000189
Ji, S., Yang, D., Lee, J., Choi, S. H., Kim, H., & Kang, K. M. (2022). Synthetic MRI: Technologies and applications in neuroradiology. Journal of Magnetic Resonance Imaging, 55(4), 1013–1025. https://doi.org/10.1002/jmri.27440
Kvernby, S., Warntjes, M. J. B., Haraldsson, H., Carlhäll, C.-J., Engvall, J., & Ebbers, T. (2014). Simultaneous three-dimensional myocardial T1 and T2 mapping in one breath hold with 3D-QALAS. Journal of Cardiovascular Magnetic Resonance: Official Journal of the Society for Cardiovascular Magnetic Resonance, 16(1), 102. https://doi.org/10.1186/s12968-014-0102-0
Yarnykh, V. L. (2007). Actual flip-angle imaging in the pulsed steady state: a method for rapid three-dimensional mapping of the transmitted radiofrequency field. Magnetic Resonance in Medicine, 57(1), 192–200. https://doi.org/10.1002/mrm.21120