Subjects

Infants were recruited and imaged at the Evelina Newborn Imaging Centre, St Thomas’ Hospital, London, UK. The study was approved by the UK Health Research Authority (Research Ethics Committee reference number: 14/LO/1169) and written parental consent was obtained in every case for imaging and data release. The images included in this release were obtained from 783 subjects born between 23-44 gestational weeks: 578 born and scanned at term-equivalent age which we defined as 37-44 weeks, 156 preterm-born subjects scanned soon after birth and 133 preterm-born subjects scanned at term-equivalent age. The images have been reviewed for evidence of anomalies and abnormalities and a radiology score is provided, although users should verify that data they use are fit for their purposes.

Overview of data

The data release contains structural (T1w and T2w) resting state functional and diffusion images supplied as original image data and after preprocessing pipelines as described below have been applied. The neonatal brain has different tissue properties to adult brain, most strikingly it has a higher water content and myelination of white matter is incomplete. Consequently, the relaxation times T1 and T2 are longer than in adult brain and white matter has longer T1 and T2 than grey matter. In neonates, brain anatomy is revealed more clearly in T2w than T1w images and thus the former are treated as the primary data for anatomical segmentation and to provide the anatomical substrates needed for functional and diffusion analysis. All neonates (with 6 exceptions) were imaged in natural sleep. If the baby woke up scanning was halted and attempts made to re-settle the subject without taking them out of the patient immobilization system. Even when sleeping peacefully, many babies move and so all data were motion corrected, mostly using methods developed specifically for the dHCP project. As a result of the challenges of imaging unsedated infants we were not able to obtain high quality and complete data for every modality on every subject.

There were 886 sessions with T2w images that passed QC and an additional session without T2w images. Of those 887 sessions, 818 had fMRI data that passed QC and 758 had dMRI data that passed QC. The T1w images were not subject to the same level of systematic QC as they were not processed by pre-processing pipelines. Because of their lower anatomical importance, the T1w images were placed at the end of the protocol and are of more variable quality than the T2w data. The release contains 711 sessions with T1w multi-slice fast spin-echo images and 734 sessions with T1 MPRAGE images.

There is a spread of gestational ages with 578 subjects in the term equivalent age range, which we defined as 37 to 44 gestational weeks. Also, although these subjects were recruited as “normal subjects” (with clearly specified inclusion and exclusion criteria), there were inevitably incidental findings on the images obtained. All the anatomical images were reviewed by an expert perinatal neuroradiologist who scored the subjects using a 5-point scale (see below) – this information is provided

Acquisition details

Imaging was carried out on 3T Philips Achieva (running modified R3.2.2 software) using a dedicated neonatal imaging system which included a neonatal 32 channel phased array head coil1. Infants were imaged without sedation except for 6 who are indicated. Anatomical images (T1w and T2w), resting state functional (rs-fMRI) and diffusion (dMRI) acquisitions were acquired in a total examination time of 63 minutes. Sequence parameters were as follows:

Calibration scans: B0 mapping was performed using an interleaved dual TE spoiled gradient echo sequence and localised image-based shimming performed for use with all EPI sequences as described in2. B0 field maps using the optimised higher order shims were subsequently re-acquired between the fMRI and dMRI acquisitions. B1 mapping was performed using the dual refocusing echo acquisition mode (DREAM)3 method, with STE first and STEAM flip angle of 60.

Anatomical acquisition: T2w and inversion recovery T1w multi-slice fast spin-echo images were each acquired in sagittal and axial slice stacks with in-plane resolution 0.8x0.8mm2 and 1.6mm slices overlapped by 0.8mm (except in T1w Sagittal which used a slice overlap of 0.74mm). Other parameters were – T2w: 12000/156ms TR/TE, SENSE factor 2.11 (axial) and 2.60 (sagittal); T1w: 4795/1740/8.7ms TR/TI/TE, SENSE factor 2.27 (axial) and 2.66 (sagittal). In addition, 3D MPRAGE was acquired with 0.8mm isotropic resolution and parameters: 11/4.6/1400ms TR/TE/TI, SENSE factor 1.2 (RL).

rs-fMRI: High temporal resolution fMRI developed for neonates4 used multiband (MB) 9x accelerated echo-planar imaging and was collected for 15 minutes, TE/TR=38/392ms gave 2300 volumes, with an acquired resolution of 2.15mm isotropic. No in-plane acceleration or partial Fourier was used. Single-band reference scans were also acquired with bandwidth matched readout, along with additional spin-echo acquisitions with both AP/PA fold-over encoding directions.

Physiological recordings of VCG, PPU and respiratory traces are provided unprocessed in the sourcedata folder. Alignment to rs-fMRI data can be achieved by means of locating the ‘end of scan’ marker (scripts are available to aid loading and interpretation of this file5), and knowing the frequency of the recordings (496Hz) and TR x number of volumes acquired (0.392s x 2300) in order to identify the start of scan point. Note, for improved accuracy on this cohort a small delay of ~85ms between the true end of data acquisition and ‘end of scan’ marker has been identified, after accounting for this the precision of identifying the true start of scan in the physiological file should be of the order +/- 50ms, for a complete scan of 15 minutes duration.

dMRI: A spherically optimized set of directions on 4 shells (b0: 20, b400: 64, b1000: 88, b2600: 128)6 was split into 4 optimal subsets (one per Phase Encoding Direction). These directions were then spread temporally taking motion and duty cycle considerations into account. If the baby woke up during the diffusion scan, the acquisition could be halted and restarted (after resettling the subject) with a user defined overlap in acquired diffusion weightings7. Acceleration of MB 4, SENSE factor 1.2 and Partial Fourier 0.86 was used, acquired resolution 1.5x1.5mm, 3mm slices with 1.5mm overlap, 3800/90ms TR/TE.

References

  1. Hughes, E. J., Winchman, T., Padormo, F., Teixeira, R., Wurie, J., Sharma, M., Fox, M, Hutter, J., Cordero-Grande, L., Price, A. N., Allsop, J,, Bueno-Conde, J., Tusor, N.,, Arichi, T., Edwards, A. D., Rutherford, M. A., Counsell, S. J., and Hajnal J. V. A dedicated neonatal brain imaging system Magnetic Resonance in Medicine (2017), 78: 794-804. DOI: 10.1002/mrm.26462

  2. Gaspar, A. Improving foetal and neonatal echo-planar imaging with image-based shimming Master Thesis (2015), Universidade de Lisboa.

  3. Nehrke, K. and Börnert, P. DREAM—a novel approach for robust, ultrafast, multislice B1 mapping. Magnetic Resonance in Medicine (2012), 68: 1517-1526. DOI: 10.1002/mrm.24158

  4. Price, A.N., Cordero-Grande, L., Malik, S.J., Abaei, M., Arichi, T., Hughes, E., Rueckert, D., Edwards, A.D., Hajnal, J.V. Accelerated neonatal fMRI using multiband EPI ISMRM 2015: 3911.

  5. ReadPhilipsScanPhysLog.m by Paul Groot (MathWorks File Exchange)

  6. Tournier, J.D., Hughes, E., Turso, N., Sotiropoulos, N. S., Jbadhi, S., Andersson, J., Reuckert, D., Edwards, A. D., Hajnal, J. V. Data-driven optimisation of multi-shell HARDI ISMRM 2015: 2897.

  7. Hutter, J., Tournier J. D., Price, A. N., Cordero-Grande, L., Hughes, E. J., Malik, S., Steinweg, J., Bastiani, M., Sotiropoulos, S. N., Jbabdi, S., Andersson, J., Edwards, A. D., and Hajnal, J. V. Time-efficient and flexible design of optimised multi-shell HARDI diffusion Magnetic Resonance in Medicine (2018), 79: 1276-1292. DOI: 10.1002/mrm.26765