The full UKB neuroimaging protocol can be found online (https://biobank.ctsu.ox.ac.uk/crystal/crys-tal/docs/brain_mri.pdf ).79 (link) MR images were acquired on a 3-T Siemens Skyra MRI scanner (Siemens, Erlangen, Germany). T1-weighted MRI used a 3D MPRAGE sequence with 1-mm isotropic resolution with the following sequence parameters: repetition time = 2000 ms, echo time = 2.01 ms, 256 axial slices, slice thickness = 1 mm, and in-plane resolution = 1 × 1 mm. In the HCHS, MR images were acquired as well on a 3-T Siemens Skyra MRI scanner. Measurements were performed with a protocol as described in previous work.74 (link) In detail, for 3D T1-weighted anatomical images, rapid acquisition gradient-echo sequence (MPRAGE) was used with the following sequence parameters: repetition time = 2500 ms, echo time = 2.12 ms, 256 axial slices, slice thickness = 0.94 mm, and in-plane resolution = 0.83 × 0.83 mm.
Skyra mri scanner
Manufactured by Siemens
Sourced in Germany
The Skyra MRI scanner is a medical imaging device manufactured by Siemens. It is designed to perform magnetic resonance imaging (MRI) examinations. The Skyra MRI scanner uses strong magnetic fields and radio waves to generate detailed images of the body's internal structures.
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Lab products found in correlation
32 channel head coil, by Siemens (10 mentions)
Neurovascular head coil, by GE Healthcare (2 mentions)
Excite hd scanner, by GE Healthcare (2 mentions)
20 channel head coil, by Siemens (2 mentions)
64 channel head coil, by Siemens (2 mentions)
Prisma mri scanner, by Siemens (1 mentions)
16 channel head coil, by Siemens (1 mentions)
20 channel coil, by Siemens (1 mentions)
32 channel receiving head coil, by Siemens (1 mentions)
20 channel head and neck coil, by Siemens (1 mentions)
Achieva 3.0 tesla mri scanner, by Philips (1 mentions)
Syngo workstation, by Siemens (1 mentions)
Trio 3t scanner, by Siemens (1 mentions)
3t trio, by Siemens (1 mentions)
64 channel head and neck coil, by Siemens (1 mentions)
Syngo mr d13, by Siemens (1 mentions)
20 channel head neck coil, by Siemens (1 mentions)
82 protocols using skyra mri scanner
1
UK Biobank 3T MRI Neuroimaging Protocol
2
3T MRI Brain Imaging Protocol
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The full UKB neuroimaging protocol can be found online (https://biobank.ctsu.ox.ac.uk/crystal/crystal/docs/brain_mri.pdf ; Miller et al., 2016 (link)). MR images were acquired on a 3 T Siemens Skyra MRI scanner (Siemens, Erlangen, Germany). T1-weighted MRI used a 3D MPRAGE sequence with 1 mm isotropic resolution with the following sequence parameters: repetition time = 2000 ms, echo time = 2.01 ms, 256 axial slices, slice thickness = 1 mm, and in-plane resolution = 1 × 1 mm. In the HCHS, MR images were acquired as well on a 3 T Siemens Skyra MRI scanner. Measurements were performed with a protocol as described in previous work (Petersen et al., 2020 (link)). In detail, for 3D T1-weighted anatomical images, rapid acquisition gradient-echo sequence (MPRAGE) was used with the following sequence parameters: repetition time = 2500 ms, echo time = 2.12 ms, 256 axial slices, slice thickness = 0.94 mm, and in-plane resolution = 0.83 × 0.83 mm.
3
Visual Stimuli Presentation and fMRI Acquisition
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Participants viewed the visual stimuli via a mirror attached on a head coil; we used PsychoPy (v. 3) to present stimuli [24 (link)]. Two response grips were used (NordicNeuroLab). We acquired imaging data of high resolution T1-weighted three-dimensional anatomical images (TR 2500 ms, TE 4.37 ms, 256 × 256 mm 100% field of view (FOV), 1 mm slice thickness), gradient-echo fieldmaps (same slice as the echo-planar imaging (EPI) images, resolution 3 × 3 mm, TR 599 ms, TE1 5.19 ms, TE2 7.65 ms, flip angle 60°, bandwidth 260, TA 1 m in 15 s), and gradient EPI functional images (TR 2260 ms, TE 27 ms, 192 mm 100% FOV, in-plane resolution 3 × 3 mm, 3 mm slice thickness, no gap, flip angle 80°, slice order = Siemens ascending interleaved), using a 3 T Siemens Skyra MRI scanner (Siemens Healthineers, Erlangen, Germany).
4
Quantitative MRI Assessment of Liver Disease
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The mpMR scanning protocol was installed, calibrated and phantom tested on a 3 T Siemens Prisma MRI scanner (Siemens Healthcare GMBH, Erlangen, Germany) at the Oxford Centre for Magnetic Resonance (OCMR) and a 3 T Siemens Skyra MRI scanner (Siemens Healthcare GMBH, Erlangen, Germany) at Alliance Medical, London. Four single transverse slices were captured throughout the liver centred at the porta hepatis. Anonymised MR data were analysed off-site using LiverMultiScan® software (Perspectum Ltd., United Kingdom) by specialised imaging analysts trained in abdominal anatomy and artefact detection. cT1 maps of the liver were delineated into whole liver segmentation maps using a semi-automatic method, as extensively described by Bachtiar and colleagues,19 and expressed as the median value within the map. cT1 interquartile range (IQR), a measure of the spread of cT1 values across the liver, and the count (expressed as a percentage) of the pixels in the liver map above a pre-defined threshold of 800 ms (pcT1), both of which represent disease heterogeneity, were also extracted from the whole liver segmentation maps. The mpMR analysis was completed by analysts blinded to the clinical data.
5
Multimodal Neuroimaging Protocol for Concussion
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All MRI Exams for the concussed patients and control volunteers were performed between February 17, 2016, and May 14, 2019, on the same 3T Siemens Skyra MRI Scanner using a 20 channel Head/Neck Coil using the following imaging protocol: T1-MPRAGE (208 slices; 1x1x1 mm, TR = 1,200 ms, TE = 2.29 ms, TI = 600 ms), FOV = 250 mm, Flip angle = 8 degrees, 3D AXIAL SWI (88 slices/1.5 mm slice thickness (interleaved)/FOV 220 mm, TR 27 ms, TE 29 ms, 1 average), DOUBLE IR (FLAIR)-Fat-sat FLAIR 120 slices, 1.4 mm slice thickness, FOV 260 mm, TR 7,500 ms, TE 321 ms, TI 1: 3,000 ms; TI 2: 450 ms, 1 average, Acceleration factor 2, ref lines 24, Turbo Factor 256.
DTI acquisition parameters were AXIAL DTI/ TA: 10:14 min,70 slices, FOV 256, 2 mm slice thickness, TR 9,000 ms, TE 88 ms, Flip Angle 15°, 1 average, Acceleration Factor 2/ref lines 24, Diffusion directions 64, b-value 1: 0 s/mm2; b-value 2: 1,000 s/mm2 GRE Field Mapping for geometric and eddy current corrections 86 slices, FOV 256 mm, 2 mm slice thickness, TR 838 ms, TE1: 4.92 sec, TE2: 7.38 ms, Flip angle: 60°. All image sets used in this study were anonymized.
DTI acquisition parameters were AXIAL DTI/ TA: 10:14 min,70 slices, FOV 256, 2 mm slice thickness, TR 9,000 ms, TE 88 ms, Flip Angle 15°, 1 average, Acceleration Factor 2/ref lines 24, Diffusion directions 64, b-value 1: 0 s/mm2; b-value 2: 1,000 s/mm2 GRE Field Mapping for geometric and eddy current corrections 86 slices, FOV 256 mm, 2 mm slice thickness, TR 838 ms, TE1: 4.92 sec, TE2: 7.38 ms, Flip angle: 60°. All image sets used in this study were anonymized.
6
High-Resolution Structural and Functional MRI
7
Multimodal Neuroimaging in Traumatic Brain Injury
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Acute phase non-contrast head CT was performed as part of the clinical assessment (6 (link)) and head MRI obtained within 72 h in participants with blood drawn. All subjects included underwent a standardized brain MRI scan within this timeframe (33 (link)). Since MRI has been shown to be more sensitive to intracranial traumatic findings (33 (link)), the results from the clinical MRI readings were used here. All MRI scans were acquired with the same protocol on the same 3.0 Tesla Siemens Skyra MRI scanner with a 32-channel head coil. The protocol included 3D volumes with T1-weighted (Magnetization Prepared Rapid Acquisition Gradient Echo), T2-weighted, Fluid-attenuated inversion recovery, and susceptibility-weighted scans. The clinical scans were read by neuroradiologists according to standard criteria, and the inter-rater reliability was moderate to good (33 (link)). Traumatic axonal injury (TAI) was diagnosed and graded as described previously (37 (link)). More detailed patient MRI results and their development over time are presented in Einarsen et al. (33 (link)).
8
Functional and Anatomical Imaging of the Striatum
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Functional (EPI sequence; 37 slices covering whole cerebrum; resolution 3 × 3 × 3 mm3 with no gap; repetition time (TR) 2.0 s; echo time (TE) 28 ms; flip angle 71°) and anatomical (MPRAGE sequence; 256 matrix; 0.9 × 0.9 × 0.9 mm3 resolution; TR 2.3 s; TE 3.08 ms; flip angle 9°) images were acquired using a 3T Skyra MRI scanner (Siemens, Erlangen, Germany). Data were processed using MATLAB and SPM8 (Wellcome Trust Centre for Neuroimaging, UCL). Functional data from one participant contained unusually extensive dropout artefacts in much of the brain including the striatum and were thus excluded from further analysis. Functional data were motion corrected prospectively during scanning and retrospectively using SPM. Low-frequency drifts were removed with a temporal high-pass filter (cutoff of 0.0078 Hz). The data were spatially smoothed using an 8-mm FWHM Gaussian kernel. Images were normalized to Montreal Neurological Institute (MNI) coordinates. MNI coordinates provided by the MNI space utility (http://www.ihb.spb.ru/~pet_lab/MSU/MSUMain.html ), which correspond to the Caudate and Putamen labels in the Talairach atlas (www.talairach.org ), were used to restrict analysis to grey matter within the striatum.
9
Multimodal Neuroimaging Protocol for Brain Analysis
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The initial 73 scans were performed on a 1.5-T EXCITE HD scanner with twin-speed gradients using a neurovascular head coil (GE Healthcare, Milwaukee, WI). High-resolution T1 anatomic images were obtained using a three-dimensional (3D) volumetric inversion recovery spoiled grass gradient recalled sequence (repetition time [TR] 7.36 ms; echo time [TE] 2.02 ms; inversion time [TI] 600 ms; flip angle [FA] 20°; 124 slices: field of view 24 cm, matrix size 256 × 256, 1.5-mm slice thickness). Fluid-attenuated inversion recovery images were acquired in the axial plane (TR 8,002 ms; TE 101.29 ms; TI 2,000 ms; FA 90°; field of view 24 cm; matrix size 256 × 256; 3-mm slice thickness). Because of a change in scanners at the WFSM Center for Biomolecular Imaging, the subsequent 190 scans were performed on a 3.0-T) Skyra MRI scanner (Siemens Healthcare, Erlangen, Germany) using a high-resolution 20-channel head/neck coil. T1-weighted anatomic images were obtained using a 3D volumetric magnetization-prepared rapid acquisition gradient echo sequence (TR 2,300 ms; TE 2.99 ms; TI 900 ms; FA 9°; 192 slices; voxel dimension 0.97 × 0.97 × 1 mm). Fluid-attenuated inversion recovery images were acquired using a 3D SPACE inversion recovery sequence (TR 6,000 ms; TE 283 ms; TI 2,200 ms; FA 120°; 160 slices; voxel dimensions 1.1 × 1.1 × 1 mm).
10
Structural MRI Acquisition Protocol
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MRI data were acquired from all participants at three imaging centers (Cheadle, Newcastle, and Reading) using an identical 3T Siemens Skyra MRI scanner (software VD13) equipped with the standard Siemens 32‐channel head coil. In Appendix S1 , we provide the bar plots with the number of subjects and percentages for each group.
The images were acquired based on T1‐weighted imaging data (3D MPRAGE, sagittal, R = 2, TI/TR = 880/2000 ms; voxel size = 1 × 1 × 1 mm; matrix size = 208 × 256 × 256) and T2‐weighted FLAIR imaging data (3D SPACE, sagittal, R = 2, PF 7/8, fat sat, TI/TR = 1800/5000 ms, elliptical acquisition; voxel size = 1.05 × 1 × 1 mm; matrix size = 192 × 256 × 256).
All the images used in this study, which were labeled as usable by the UK Biobank, were defaced and registered between modalities (Alfaro‐Almagro et al., 2018 (link)).
The images were acquired based on T1‐weighted imaging data (3D MPRAGE, sagittal, R = 2, TI/TR = 880/2000 ms; voxel size = 1 × 1 × 1 mm; matrix size = 208 × 256 × 256) and T2‐weighted FLAIR imaging data (3D SPACE, sagittal, R = 2, PF 7/8, fat sat, TI/TR = 1800/5000 ms, elliptical acquisition; voxel size = 1.05 × 1 × 1 mm; matrix size = 192 × 256 × 256).
All the images used in this study, which were labeled as usable by the UK Biobank, were defaced and registered between modalities (Alfaro‐Almagro et al., 2018 (link)).
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