Magnetic Resonance Imaging was performed on a 3T system (Philips Healthcare, Best, the Netherlands) with a body coil for radiofrequency transmission and an 8-channel head coil with parallel imaging capability for signal reception. Foam padding was used to stabilize the head and minimize head motion. The MRI protocol consisted, among other sequences, of a T1-weighted magnetization-prepared rapid acquisition of gradient echo sequence (T1-MPRAGE) and a pCASL sequence (17 (link)). The scan parameters of the T1-MPRAGE sequence were as follows; TR/TE/TI = 8.1 ms/3.7 ms/1100 ms, shot interval 2100 ms, flip angle = 18°, voxel size 1×1×1 mm3, number of slices 160, sagittal slice orientation and duration 3 min and 57s. Scan parameters of the pCASL sequence were: FOV = 240×240 mm2, matrix = 80×80, 27 axial slices, thickness = 5mm, TR/TE = 4020 ms/14 ms, labeling duration = 1.65s, post-labeling delay = 1.5 s, single-shot echo-planar imaging (EPI), 30 pairs of label and control images, and duration 4 min. The post-labeling delay was slightly shorter than that recommended in the ‘ASL white paper’ (18 (link)) because the study started in 2008, seven years before the white paper was published.
3t system
Manufactured by Philips
The 3T system is a magnetic resonance imaging (MRI) device manufactured by Philips. It provides a magnetic field strength of 3 Tesla, which is used to generate high-quality images of the human body for medical diagnostic purposes.
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Lab products found in correlation
1.5t system, by GE Healthcare (2 mentions)
Magnevist, by Bayer (1 mentions)
32 channel sense head coil, by Philips (1 mentions)
32 channel quadrature volume head coil, by Philips (1 mentions)
8 channel sense head coil, by Philips (1 mentions)
Gyroscan intera 1.5t, by Philips (1 mentions)
3t intera, by Philips (1 mentions)
32 channel head coil, by Philips (1 mentions)
16 protocols using 3t system
1
3T MRI Acquisition Protocol for Perfusion and Structural Imaging
2
Cardiac MRI Examination Protocol for Acute Myocardial Infarction
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The ECG-gated CMR examinations were performed using a 3-T system (Philips Healthcare, Best, The Netherlands) within seven days of the onset and at the six-month follow-up visit. The CMR protocol included a localizer, T2-weighted, cine, first-pass perfusion, and delay-enhancement sequences. Each long-axis slice was subjected to balanced, steady-state free precision (bSSFP) cines (with a 60° separation around the long axis of the LV (two, three, and four chambers)). A total of 10–12 continuous slices of short-axis cines were obtained after the injection of the contrast agent (gadolinium, 0.2 mmol/kg), covering the entire LV region from the ring of the mitral valve to the apex (parallel slices 8 mm wide without gap; TE = 1.6 ms, TR = 3.2 ms, flip angle 45, voxel size 2.0 × 1.6 × 8 mm3, field of view 350 × 350 mm; 30 phases in each cardiac cycle). The gadolinium enhancement sequences were acquired 10 min after the contrast injection (Magnevist, Bayer Healthcare, Berlin, Germany).
3
3T MRI Multimodal Neuroimaging Protocol
4
High-resolution MRI Acquisition Protocol
5
Whole-Brain Diffusion Imaging on 3T MRI
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MRI was performed on a 3T system (Philips Achieva) equipped with a 32-channel quadrature volume head coil. Head movement was minimized by foam padding within the coil and scanner noise was attenuated using a combination of earplugs and circumaural headphones. Whole brain diffusion imaging data was acquired using a single-shot spin echo EPI sequence: repetition time = 7748 ms, echo time = 86 ms, flip angle = 90°, field of view = 224 × 224 mm, voxel size = 2 mm isotropic with no gap between slices (n = 60), diffusion gradient (monopolar) directions = 64, diffusion gradient timing DELTA/delta = 42.4/10 ms, b-values: 0, 1000 s/mm2, fat suppression using SPIR, in-plane, SENSE factor = 2.
6
Multi-Modal Neuroimaging: Diffusion Tensor Imaging and T1-Weighted MRI
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Scanning was performed on a Philips 3 T system (Achieva, Philips, Best, The Netherlands), using a dedicated 8-channel phased-array headcoil. T1-weighted and DTI images were acquired in a single scanning session for each participant.
Diffusion-weighted imaging was performed using a spin-echo single-shot echo-planar imaging sequence, with TR/TE = 11,031/55 ms, number of excitations (NEX) = 1 and an isotropic voxel size of 2 × 2 × 2 mm. Fifty-six contiguous axial slices were positioned to cover the whole brain. Images were acquired for 32 non-collinear directions of the diffusion gradients (with b = 1000 s/mm2, using a Philips default diffusion vector scheme) and one image was acquired with no diffusion weighting (b = 0, b0 image), allowing for computation of the diffusion tensor. Parallel acquisition (SENSE factor = 1.5) and partial k-space sampling (factor = 0.68) were used. The total scanning time was 7′33″.
In addition, a high-resolution high-contrast anatomical T1-weighted scan was acquired for hippocampal GM volumetry purposes. A 3D TFE gradient-echo sequence was used, with TR/TE = 8.3/3.8 ms, NEX = 1 and an isotropic voxel size of 1 × 1 × 1 mm. One hundred and sixty coronal slices were acquired, covering the whole brain.
Diffusion-weighted imaging was performed using a spin-echo single-shot echo-planar imaging sequence, with TR/TE = 11,031/55 ms, number of excitations (NEX) = 1 and an isotropic voxel size of 2 × 2 × 2 mm. Fifty-six contiguous axial slices were positioned to cover the whole brain. Images were acquired for 32 non-collinear directions of the diffusion gradients (with b = 1000 s/mm2, using a Philips default diffusion vector scheme) and one image was acquired with no diffusion weighting (b = 0, b0 image), allowing for computation of the diffusion tensor. Parallel acquisition (SENSE factor = 1.5) and partial k-space sampling (factor = 0.68) were used. The total scanning time was 7′33″.
In addition, a high-resolution high-contrast anatomical T1-weighted scan was acquired for hippocampal GM volumetry purposes. A 3D TFE gradient-echo sequence was used, with TR/TE = 8.3/3.8 ms, NEX = 1 and an isotropic voxel size of 1 × 1 × 1 mm. One hundred and sixty coronal slices were acquired, covering the whole brain.
7
High-Resolution 3T MRI Brain Imaging
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MRI scans were obtained with a 3-T system (Philips Medical Systems, Best, The Netherlands) using the same sequence for both baseline and follow-up scans: TR = 6.39 ms, TE = 2.9 ms, flip angle = 8°, matrix size = 256 × 256, FOV = 256 × 256 × 190 mm, and slice thickness = 1 mm with no gap, yielding 1 × 1 × 1 mm3 isotropic voxels.
8
Multi-modal MRI Brain Imaging Protocol
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All participants were scanned on a 3T system (Philips Achieva) using an 8-channel SENSE head coil. Data for R2* mapping were collected using a three dimensional gradient-echo sequence with five echoes (TR = 28 ms, TE1 = 5 ms, echo spacing = 5 ms, α = 17°, field of view = 230 x 165 x 110 mm3, acquired voxel size = 0.9 x 1 x 1.6 mm3, reconstructed voxel size = 0.8 x 0.8 x 0.8 mm3). DTI data were acquired using a spin echo planar sequence with b0 = 0, b1 = 1000, 16 directions, TR/TE = 7465/75 ms, FOV = 212 x 212 mm2, 60 slices of 2.2 mm thickness, in-plane resolution = 2.2 x 2.2 mm2. Three-dimensional T1 and T2 weighted scans were collected for image registration purposes and WM segmentation with the following parameters: 3D T1-weighted sequence: voxel size = 1.0 x 1.0 x 1.6 mm3, reconstructed to 0.8 x 0.8 x 0.8 mm3, FOV = 256 x 256 x 160 mm3, TR/TE = 7.6/3.7 ms. 3D T2-weighted scan: voxel size = 1.0 x 1.0 x 1.6 mm3, reconstructed to 0.8 x 0.8 x 0.8 mm3, FOV = 256 x 256 x 160 mm3, TR/TE = 2500/363 ms.
9
Neonatal Brain MRI Injury Assessment
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Structural MRI was performed on a 3T system (Philips Medical Systems, Best, The Netherlands) between postnatal day 4 and 13 (please see Supplementary Information for further details). MRI findings were classified according to the National Institute of Child Health and Human Development Neonatal Research Network 6-point injury score (Shankaran et al., 2017 (link), Shankaran et al., 2012 (link)).
10
Healthy Brain MRI Dataset Analysis
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All HCs come from the IXI (Information eXtraction from Images) Dataset (http://brain-development.org/ixi-dataset/ ). The dataset includes nearly 600 MR images from normal, healthy subjects. The MR image acquisition protocol for each subject included T1-, T2- and proton density (PD)-weighted images, magnetic resonance angiography (MRA) images and diffusion-weighted images (15 directions). We used T1 images from 32 age-matched subjects from Hammersmith Hospital using a Philips 3T system. The details of the scanner parameters are as follows: TR = 9.6, TE = 4.60, number of phase encoding steps = 208, echo train length = 208, reconstruction diameter = 240.0, acquisition matrix = 208 × 208, and flip angle = 8.0°.
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