DOI: 10.60641/ecxz-6z12
title: Structural Magnetic Resonance Imaging (MRI)

description: YOUth is a large-scale longitudinal cohort study following children from the city of Utrecht and its surrounding areas in their development from pregnancy until early adulthood. The YOUth cohort focuses on neurocognitive development involved in two core characteristics of behavioral development: social competence and behavioral control. YOUth includes children from the general population to cover the whole range of variation in behavioral development, ranging from uncomplicated development, through problem behavior, to psychiatric disorders. To understand why some children develop problematic behavior, and others show resilience, YOUth measures a broad range of biological, child-related and environmental determinants.

YOUth conducts repeated measurements at regular intervals (i.e. 'waves'). Specifically, the study has two inclusion moments: YOUth Baby & Child and YOUth Child & Adolescent. YOUth applies a flexible longitudinal design to the cohorts, meaning that children are measured at broader age ranges (3-year age ranges) at each wave. The main benefit of the flexible age design is that it provides more detailed information on the neurodevelopmental curves over time.

An extensive data set is generated, including 3D-ultrasound sweeps of the fetal brain, eye tracking, EEG, (f)MRI, computer tasks, cognitive measurements and parent-child observations. We also collect a broad range of questionnaires on behavior, personality, health, lifestyle, parenting, child development, use of (social) media and more. Finally, (umbilical) blood samples, buccal swabs, saliva and hair samples are collected at each visit, and stored in the UMC Utrecht Biobank.
description: Structural magnetic resonance imaging (MRI) is a non-invasive technique for examining the anatomy and pathology of the brain (as opposed to using functional magnetic resonance imaging [fMRI] to examine brain activity).
description: In the YOUth Baby and Child cohort, fetal MRI (T2) in the mother consisted of coronal, saggital and/or axial T2-weighted turbo fast spin-echo sequences with the following parameters: 80 2.5mm slices; echo time (TE) 180 ms; repetition time (TR) 55321 ms; flip angle 110 degrees; in-plane voxel size 1.25 x 1.25mm^2. The raw Philips DICOM files were converted to NIfTi format via dcm2niix (v20190112, https://github.com/rordenlab/dcm2niix) and 3D reconstructed with the dHCP method (https://github.com/SVRTK/SVRTK). We visually checked the scans and segmentations for quailty. Neonatal MRI (T1 and T2) in the newborn child consisted of a T2-weighted turbo fast spin-echo sequence with the following parameters: 110x1.2mm slices; echo time (TE) 150 ms; repetition time (TR) 4851 ms; flip angle 90 degrees; in-plane voxel size 1.2 x 1.2mm^2. The raw Philips DICOM files were converted to NIfTi format via dcm2niix (v20190112, https://github.com/rordenlab/dcm2niix) and volumes were calculated with the dHCP method (https://github.com/BioMedIA/dhcp-structural-pipeline). We visually checked the scans and segmentations for quailty. In the YOUth Child and Adolescent cohort, adolescent MRI (T1) consisted of a T1-weighted 3D fast-field echo scan with the following parameters: 200 0.8 mm contiguous slices; echo time (TE) 4.6 ms; repetition time (TR) 10ms; flip angle 8°; in-plane voxel size 0.75 × 0.75 mm^2. The raw Philips DICOM files were converted to NIfTi format via dcm2niix (v20190112, https://github.com/rordenlab/dcm2niix) using the flag '-p n' (no Philips precise float scaling), and subsequently defaced using mri_deface (v1.22, https://surfer.nmr.mgh.harvard.edu/fswiki/mri_deface), resulting in 4-byte float gzipped NIfTi files.