Scans for both studies were acquired at CRICBristol, University of Bristol, UK, on the same Siemens Magnetom Skyra 3T system equipped with a parallel transmit body coil and a 32-channel head receiver array coil. The two studies used similar, but slightly different scanning protocols.
3t skyra system
Manufactured by Siemens
Sourced in Germany
The 3T Skyra system is a high-performance magnetic resonance imaging (MRI) scanner designed by Siemens for clinical and research applications. It operates at a magnetic field strength of 3 tesla, providing high-quality imaging capabilities. The system is equipped with advanced hardware and software features to enable comprehensive diagnostic examinations.
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22 protocols using 3t skyra system
1
Siemens Magnetom Skyra 3T Imaging Protocol
2
Multimodal MRI Neuroimaging Protocol for Pediatric Populations
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MRI was performed on a Skyra 3-T system (Siemens Healthineers, Erlangen, Germany) with a 64-element or an 8-element neonatal head coil (babies <2 months). The MP2RAGE sequence took 5 min, 47 s (sagittal, voxel size 1×1×1 mm3, field of view 256 mm2, repetition time [TR]=5,000 ms, echo time [TE]=2.98 ms, TI1=700 ms, TI2=2,500 ms, flip angle1=4°, flip angle2=5°, 7.1 ms echo spacing, 176 slices, generalized autocalibrating partial parallel acquisition [GRAPPA] acceleration factor 3). The MRI protocol also included an axial, two-dimensional (2-D), fat-saturated T2 turbo spin echo (TSE) sequence (voxel size 0.4×0.4×3 mm3; field of view 230 mm2; TR=5,000 ms; TE=100 ms; flip angle=150°; GRAPPA acceleration factor 2; duration 2 min, 12 s) and sagittal MP-RAGE (voxel size 0.9×0.9×0.9 mm3, field of view 240 mm2, TR=2,300 ms, TE=2.32 ms, TI=900 ms, flip angle=8°, GRAPPA acceleration factor 2) as well as 2-D or three-dimensional (3-D) T2 fluid-attenuated inversion recovery (FLAIR), T2*, and diffusion-weighted imaging (DWI) sequences. Contrast agent was rarely administered for the MP-RAGE, but never for the MP2RAGE. MRI was usually performed under sedation (50–100 mg/kg chloralhydrate perorally) in children <4 years old and in general anesthesia (combined intravenous propofol and isoflurane per inhalation) for older children if necessary.
3
MRI Acquisition of Anatomical and Functional Brain Data
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MRI was performed on a Siemens Magnetom Skyra 3T system (Erlangen, Germany). In the first scanning session, high-resolution T1-weighted images were acquired for anatomical reference (anatomical scan) with acquisition parameters: MP2RAGE sequence, 1 mm isotropic voxels, matrix size = 240 × 256 × 176, repetition time (TR) = 5000 ms, echo time (TE) = 2.98 ms, inversion time (TI) = 700 ms & 2500 ms, flip angle (FA) = 4° & 5°, and GRAPPA using an iPAT factor of 2. Functional scans were acquired in both scanning sessions with acquisition parameters: Gradient echo (GE) echo planar imaging (EPI) sequence, 3 mm isotropic voxels, matrix size = 64 × 64 × 29, TR = 1500 ms, TE = 27 ms, FA = 60° and GRAPPA using an iPAT factor of 3.
4
Multi-modal MRI Acquisition Protocol for Hippocampal Imaging
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All MRI scans were undertaken using a Siemens Magnetom Skyra 3T system. The system was also equipped with a 32-channel head receiver array coil and a parallel transmit body coil. The imaging protocol used in this study was as follows:
3D T1-weighted Magnetisation-Prepared Rapid Gradient Echo (MPRAGE) with the parameters: sagittal, TR 2200 ms, TE 2.28 ms, TI 900 ms, flip angle 9°, FOV 220 × 220 × 179 mm, acquired resolution 0.86 × 0.86 × 0.86 mm, acquired matrix size 256 × 256 × 208, acquisition time 5 min and 7s. Multi-contrast TSE with the parameters: Coronal, TR 7500ms, number of echoes: 3, TE 9.1, 72 & 136 ms, acquired resolution 0.69 × 0.69 × 1.5 mm, reconstructed resolution 0.34 × 0.34 × 1.5 mm (after 2-fold interpolation in-plane by zero-filling in k-space, and inclusive of 15% slice gap), GRAPPA factor 2, FOV 220 × 220 × 34, acquired matrix size 270 × 320 × 58, acquisition time 5-min and 9s. Note: this scan was not ‘whole-brain’, it’s coverage only extending approx. 1cm beyond anterior and posterior ends of the hippocampus. These scans were tilted such that the hippocampal body lay perpendicular to the slice acquisition plane.
3D T1-weighted Magnetisation-Prepared Rapid Gradient Echo (MPRAGE) with the parameters: sagittal, TR 2200 ms, TE 2.28 ms, TI 900 ms, flip angle 9°, FOV 220 × 220 × 179 mm, acquired resolution 0.86 × 0.86 × 0.86 mm, acquired matrix size 256 × 256 × 208, acquisition time 5 min and 7s. Multi-contrast TSE with the parameters: Coronal, TR 7500ms, number of echoes: 3, TE 9.1, 72 & 136 ms, acquired resolution 0.69 × 0.69 × 1.5 mm, reconstructed resolution 0.34 × 0.34 × 1.5 mm (after 2-fold interpolation in-plane by zero-filling in k-space, and inclusive of 15% slice gap), GRAPPA factor 2, FOV 220 × 220 × 34, acquired matrix size 270 × 320 × 58, acquisition time 5-min and 9s. Note: this scan was not ‘whole-brain’, it’s coverage only extending approx. 1cm beyond anterior and posterior ends of the hippocampus. These scans were tilted such that the hippocampal body lay perpendicular to the slice acquisition plane.
5
Pseudocontinuous ASL Perfusion Imaging
6
Multimodal Neuroimaging of Whole-Brain Function
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Whole-brain imaging was conducted on a Siemens Skyra 3T system with a 32-channel head coil. Functional images were acquired using a multiband (CMRR) sequence covering the whole brain (repetition time [TR] = 1400 ms, echo time [TE] = 30 ms, flip angle = 65, multiband factor = 4, 2.5 mm isotropic voxel size, 60 slices with no gap). The slice package was tilted approximately 30° relative to the AC-PC line. Structural images were acquired using a submillimeter T1-weighted magnetization prepared rapid acquisition gradient echo sequence (TR = 2200 ms, TE = 218 ms, flip angle 8, inversion time [TI] = 1000, 0.88 mm isotropic voxel size). Visual stimuli were presented using the software Presentation (Neurobehavioral System, Albany, CA, USA) and delivered via a 32″ Full HD monitor (NNL, NordicNeuroLab, Bergen, Norway) located at the back of the scanner bore. Verbal response was captured with an MR-compatible microphone system (FOMRI-III; Optoacoustics, Mazor, Israel). Button presses were collected using an MRI compatible fiber optic response pad (Current Designs Inc., Philadelphia, PA, USA).
7
Multimodal Neuroimaging Protocol for Alzheimer's Assessment
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Isometric 1 mm T1-weighted magnetic resonance imaging (MRI) was performed with a Skyra 3T system (Siemens, Erlangen, Germany).
11C-PiB PET was performed with a High Resolution Research Tomograph (ECAT HRRT, CTI/Siemens, Knoxville, TN) according to a previously published scan protocol [1 (link)]. The pretreatment scans were performed at different time before treatment start, while the posttreatment scans all were performed on the day following the end of the light-therapy, i.e., on day 11. A mean dose of 407 ± 13.8 MBq (for poststimulation scans) and 424 ± 15.3 MBq (for the prestimulation scans) 11C-PiB was injected, and list-mode PET was acquired for 40-90 minutes postinjection. Data was subsequently rebinned into five frames of 10 min each.
11C-PiB PET was performed with a High Resolution Research Tomograph (ECAT HRRT, CTI/Siemens, Knoxville, TN) according to a previously published scan protocol [1 (link)]. The pretreatment scans were performed at different time before treatment start, while the posttreatment scans all were performed on the day following the end of the light-therapy, i.e., on day 11. A mean dose of 407 ± 13.8 MBq (for poststimulation scans) and 424 ± 15.3 MBq (for the prestimulation scans) 11C-PiB was injected, and list-mode PET was acquired for 40-90 minutes postinjection. Data was subsequently rebinned into five frames of 10 min each.
8
In Vivo Measurement of Bias-Field Shifts
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All in vivo measurements were gained from five male healthy volunteers in the age between 28 and 33 with the approval of the responsible ethics committee on a Skyra 3 T system (Siemens, Erlangen, Germany). To measure the BS‐shift a GRE sequence was modified by adding an off‐resonant Gaussian shaped RF‐pulse between excitation and readout as stated in15 with a duration T pulse = 10 20 a squared FOV with 230 mm, a resolution of 2 mm in slice direction and a slice oversampling of 25%. TE and TR were set to minimal values of TE/TR = 13.5/95 ms, respectively, and an excitation flip‐angle of α = 25∘ was used which corresponds to the mean Ernst‐angle in gray and white matter. The minimal TE is restricted by the length of the BS‐pulse and the TR by the SAR‐constraint. The acquisition parameters for liver and knee dataset were adjusted to a matrix size of 128 × 128 × 44 and 128 × 128 × 52, a FOV of 220 and 150 mm and a resolution in slice direction of 3.2 and 2.5 mm, respectively.
9
Structural MRI Imaging Protocol
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Detailed descriptions of structural imaging protocols are provided on the website of the HCP (www.humanconnectome.org ) and in previous publications21 (link). In brief, two separate T1-weighted, high resolution (0.7-mm isotropic voxels) anatomical images (i.e. 3D MPRAGE) were acquired on a customized Siemens 3-T Skyra system (Siemens, Germany) with a 32-channel head coil, using the following parameters: FOV=224 mm, matrix=320, 256 sagittal slices per single slab, TR=2400 ms, TE=2.14 ms, TI=1000 ms, FA=8°, Bandwidth (BW)=210 Hz per pixel, Echo Spacing (ES) =7.6 ms. For this study we used anatomical images from the first scan only.
10
High-Resolution Diffusion Imaging Protocol
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Data were acquired on a modified 3T Skyra System (Siemens) using a 32-channel coil. A T1-weighted structural image was acquired (TR = 2400ms; TE = 2.14ms; TI = 1000ms; flip angle = 8°; voxel size = .7x.7x.7mm) [28 (link)]. Diffusion acquisition involved a spin-echo EPI sequence [29 (link), 30 (link)] with multiband EPI [31 (link), 32 ] and 270 diffusion-weighted directions (TR = 5520ms; TE = 89.5ms; flip angle = 78°; refocusing flip angle = 160°; voxel size = 1.25x1.25x1.25mm; multiband factor = 3; b-values = 1000, 2000, 3000 s/mm2) [28 (link), 33 (link)].
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