Scanning is carried out at the Oxford Centre for Functional MRI of the Brain (FMRIB) using a 3 T Siemens Magnetom Verio (Erlangen, Germany) Scanner with a 32-channel receive head coil. The neuroimaging protocol comprises both structural and functional sequences and lasts approximately 50 minutes. MRI sequences include: a) high-resolution T1-weighted, b) diffusion MRI (dMRI), c) resting-state functional MRI (rfMRI), d) Fluid Attenuated Inversion Recovery (FLAIR) and e) T2*. A full description of the MRI parameters adopted in our sequences is provided in Table 2 .
32 channel receive head coil
Manufactured by Siemens
Sourced in Germany
The 32-channel receive head coil is a specialized piece of medical imaging equipment designed for use with magnetic resonance imaging (MRI) systems. This coil is responsible for receiving the radio frequency (RF) signals generated by the body during an MRI scan, which are then processed to create detailed images of the head and brain. The 32 individual receiver channels allow for improved signal-to-noise ratio and enhanced image quality compared to lower-channel configurations.
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Lab products found in correlation
3t scanner, by Siemens (2 mentions)
Skyra 3t scanner, by Siemens (1 mentions)
Vd13a sp4, by Siemens (1 mentions)
Skyra 3t, by Siemens (1 mentions)
Magnetom trio, by Siemens (1 mentions)
Magnetom trio scanner, by Siemens (1 mentions)
Presentation software, by Neurobehavioral Systems (1 mentions)
Spike2, by Cambridge Electronic Design (1 mentions)
Power1401 3a, by Cambridge Electronic Design (1 mentions)
Body transmission coil, by Siemens (1 mentions)
3t connectome skyra, by Siemens (1 mentions)
Prisma 3t scanner, by Siemens (1 mentions)
11 protocols using 32 channel receive head coil
1
Comprehensive Neuroimaging Protocol for Brain
2
Brain Imaging Processing Protocol
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Brain MRI data including high-resolution, T1-weighted, three-dimensional MPRAGE and T2-weighted FLAIR images were acquired on a standard Siemens Skyra 3T scanner with a 32-channel receive head coil. The imaging data were processed and released as imaging-derived phenotypes. Full details of the imaging protocol and processing pipeline have been previously described [28 (link)]. We used imaging summary statistics of volumes of total brain, grey matter, white matter hyperintensity (WMH), and hippocampus. Brain tissue volumes were normalized for head size based on the external surface of the skull [28 (link)]. Median absolute deviation was used to exclude extreme outliers [29 (link)].
3
Multimodal Brain Imaging in UK Biobank
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Full details of the MRI protocol and processing steps have previously been reported (Alfaro- Almagro et al., 2018 (link); Miller et al., 2016 (link)). The UK Biobank used three dedicated imaging centres, each equipped with identical MR scanners (3.0 T Siemens Skyra, software VD13) using the standard Siemens 32-channel receive head coil. 3D MPRAGE T1-weighted volumes were both pre-processed and analysed by the UK Biobank imaging team using FSL (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki ) tools and analysis pipelines adapted from the Human Connectome Project (Miller et al., 2016 (link); Jenkinson et al., 2012 (link); Glasser et al., 2013 (link)). The current project takes advantage of the UK Biobank imaging team's release of analysed imaging data regional statistics, known as Imaging Derived Phenotypes (IDP) (Alfaro- Almagro et al., 2018 (link)).
4
UK Biobank Brain Imaging Data Protocol
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Since 2014, UK Biobank has been enhancing the dataset with imaging data that includes brain MRI.
40 (link),
44 (link) It consists of imaging‐derived phenotypes, whose acquisition and quality control have been previously described.
45 (link) Briefly, brain imaging data were obtained at 4 data collection sites (Cheadle, Newcastle, Reading and Bristol; all UK) using 3 identical scanners (3T Siemens Skyra), with a standard Siemens 32‐channel receive head coil. Preprocessing and quality control were undertaken by the UK Biobank research team according to published procedures.
45 (link) Our analyses included total brain volume, brain volumes of 68 cortical areas, 14 subcortical structures, FA and MD of 25 white matter tracts. The measures of brain volume were corrected for head size by multiplication with the T1‐based scaling factor (UK Biobank field ID 25000). The brain regions and white matter tracts used in the study are depicted in FigureS2 .
40 (link),
44 (link) It consists of imaging‐derived phenotypes, whose acquisition and quality control have been previously described.
45 (link) Briefly, brain imaging data were obtained at 4 data collection sites (Cheadle, Newcastle, Reading and Bristol; all UK) using 3 identical scanners (3T Siemens Skyra), with a standard Siemens 32‐channel receive head coil. Preprocessing and quality control were undertaken by the UK Biobank research team according to published procedures.
45 (link) Our analyses included total brain volume, brain volumes of 68 cortical areas, 14 subcortical structures, FA and MD of 25 white matter tracts. The measures of brain volume were corrected for head size by multiplication with the T1‐based scaling factor (UK Biobank field ID 25000). The brain regions and white matter tracts used in the study are depicted in Figure
5
Spinal Cord CSA Measurement in UK Biobank
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Data used for this study were unprocessed NIfTI T1w structural scans from the UK Biobank Brain Imaging dataset (Miller et al., 2016 (link)). Images were acquired in four different assessment centers on a Siemens Skyra 3T running VD13A SP4 with a standard Siemens 32-channel receive head coil. T1w structural scan has a field of view of 208 × 256 × 256 with an isotropic resolution of 1 mm3. The superior-inferior field of view of 256 mm typically covers down to C3 vertebral level, which is relevant for the present study as SC CSA was measured around the C2–C3 vertebral level. The UK Biobank data includes preprocessed data (corrected for gradient non-linearity and masked), however we could not use these data because the SC was masked out. We therefore used the unprocessed T1w images as input of the processing pipeline described in the next section.
6
MRI Brain Imaging Before Surgery
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Imaging pertinent to this study was performed before surgery on a 3T Siemens Magnetom-Trio (Erlangen, Germany) with a 32-channel receive head coil. Padding was used inside the head coil to reduce discomfort and head motion.
7
Multimodal Neuroimaging Protocol
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Imaging was performed with a 3-T Siemens MAGNETOM Trio scanner using a 32-channel receive head coil (Siemens Healthcare, Erlangen, Germany). Respiratory parameters and blood volume pulse were measured continuously (Expression; Invivo, Gainesville, FL, USA), digitised (Power 1401-3A; Cambridge Electronic Design, Cambridge, UK) and stored using Spike2 software (Cambridge Electronic Design). Presentation software (Neurobehavioral Systems) was used for stimulus presentation and a CED 1401 analogue-digital converter (Cambridge Electronic Design) was used for response logging. Each of four scanning sessions lasted ∼16 min.
8
Resting-State fMRI Acquisition Protocol
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All participants were scanned using a Siemens 3 T scanner housed at Washington University in St Louis. Scans were taken using a standard 32-channel Siemens receive head coil and a “body” transmission coil. The rsfMRI data were of approximately 15 minutes duration with eyes open and relaxed fixation on a projected bright crosshair on a dark background (in a dark room).
The structural and functional MRI images were acquired using the following parameters [48 (link)]:
Structural MRI: T1w 3D magnetization-prepared rapid acquisition with gradient echo (MPRAGE), Field of View: 224 × 224 mm, TR = 2400 ms, TE = 2.14 ms, Flip Angle= 8◦, Voxel size= 0.7 mm isotropic. T2W 3D T2-SPACE, Field of View: 224 × 224 mm, TR = 3200 ms, TE = 565 ms, Flip Angle= variable, Voxel size=0.7 mm isotropic.
Functional MRI: Gradient echo Echo Planar Imaging (EPI) sequence, Field of View: 208 × 180 mm (RO×PE), TR = 720 ms, TE = 33.1 ms, Flip Angle= 52◦, Voxel size: 2.0 mm isotropic, 72 slices.
The structural and functional MRI images were acquired using the following parameters [48 (link)]:
Structural MRI: T1w 3D magnetization-prepared rapid acquisition with gradient echo (MPRAGE), Field of View: 224 × 224 mm, TR = 2400 ms, TE = 2.14 ms, Flip Angle= 8◦, Voxel size= 0.7 mm isotropic. T2W 3D T2-SPACE, Field of View: 224 × 224 mm, TR = 3200 ms, TE = 565 ms, Flip Angle= variable, Voxel size=0.7 mm isotropic.
Functional MRI: Gradient echo Echo Planar Imaging (EPI) sequence, Field of View: 208 × 180 mm (RO×PE), TR = 720 ms, TE = 33.1 ms, Flip Angle= 52◦, Voxel size: 2.0 mm isotropic, 72 slices.
9
High-Resolution MRI Brain Imaging Protocol
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Participants were scanned on a Siemens 3T Connectome Skyra with a 100 mT gradient coil and a 32-channel Siemens receive head coil (Glasser et al., 2013 (link)). B0 field maps, B1- and B1 + maps were collected to correct for readout distortion and intensity inhomogeneities. T1-weighted (T1w) images were collected as a 3D single-echo magnetization prepared – rapid gradient echo (MP-RAGE) images with the following acquisition parameters: voxel size = 0.7 mm isotropic, FOV = 224 mm, matrix = 320, 256 sagittal slices per slab, TR = 2400 ms, TE = 2.14 ms, TI = 1000 ms, FA = 8°, Bandwidth = 210 Hz per pixel, echo spacing = 7.6 ms, GRAPPA factor = 2, 10% phase encoding over-sampling (A-P), dwell time = 7.4 μs. T2-weighted (T2w) images were collected as 2 variable flip angle turbo spin-echo sequences averaged together with the following acquisition parameters: voxel size = 0.7 mm isotropic, FOV = 224 mm, matrix = 320, 256 sagittal slices per slab, TR = 3200 ms, TE = 565 ms, BW = 744 Hz/pixel, no fat suppression pulse, GRAPPA = 2, turbo factor = 314, echo train length = 1105 echoes, 10% phase encoding oversampling, dwell time = 2.1 μs.
10
Standardized Neuroimaging in the HCP Cohorts
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Neuroimaging data in the HCP-YA cohort were obtained using a customised 3T Magnetic Resonance Siemens Skyra “Connectom” scanner with a standard 32-channel Siemens receive head coil in a single site at Washington University in St. Louis, United States of America55 (link),58 (link). T1-weighted images were obtained using a 3D MPRAGE sequence (TR = 2400 ms; TE = 2.14 ms; TI = 1000 ms; voxel size = 0.7 mm isotropic)55 (link),58 (link)–60 (link).
In the HCP-A cohort, neuroimaging data were acquired on standard Siemens 3T Prisma scanners with Siemens 32-channel Prisma head coils at four sites in the United States of America: Washington University in St. Louis, University of California-Los Angeles, University of Minnesota and Massachusetts General Hospital57 (link). Matched neuroimaging protocols were used across sites56 (link). T1-weighted images were obtained using multi-echo MPRAGE sequences (TR/TI = 2500/1000; TE = 1.8/3.6/5.4/7.2 ms; voxel size = 0.8 mm isotropic)57 (link).
In the HCP-A cohort, neuroimaging data were acquired on standard Siemens 3T Prisma scanners with Siemens 32-channel Prisma head coils at four sites in the United States of America: Washington University in St. Louis, University of California-Los Angeles, University of Minnesota and Massachusetts General Hospital57 (link). Matched neuroimaging protocols were used across sites56 (link). T1-weighted images were obtained using multi-echo MPRAGE sequences (TR/TI = 2500/1000; TE = 1.8/3.6/5.4/7.2 ms; voxel size = 0.8 mm isotropic)57 (link).
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