Skyra 3t scanner

Manufactured by Siemens

Sourced in Germany, United Kingdom, United States

The Skyra 3T scanner is a magnetic resonance imaging (MRI) system designed to provide high-quality imaging. It operates at a magnetic field strength of 3 Tesla, enabling enhanced image resolution and signal-to-noise ratio. The Skyra 3T scanner is a core laboratory equipment used for medical and research applications.

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207 protocols using skyra 3t scanner

MRI Brain Structures and Volumes

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Magnetic resonance imaging (MRI) data were collected from 4 imaging centers located in Cheadle, Reading, Newcastle, and Bristol. Information about image acquisition and processing is available at the UK Biobank website in the brain scan protocol and brain imaging documentation (35 (link),36 ). Briefly, participants were scanned with a Siemens Skyra 3T scanner with a standard Siemens 32-channel head coil. T1-weighted imaging (resolution: 1.0 × 1.0 × 1.0 mm; field-of-view: 208 × 256 × 256 matrix) and T2 FLAIR imaging (resolution: 1.05 × 1.0 × 1.0 mm; field-of-view: 192 × 256 × 256 matrix) were performed to provide volumes of brain tissues and structures. Summary measures of brain structure were generated by an image-processing pipeline developed and run on behalf of the UK Biobank, using publicly available image-processing tools (the FMRIB Software Library, version 5.0.10 and FreeSurfer, version 6.0) (37 (link)).
In this study, the volumes (in cubic millimeters) of total brain, gray matter, white matter, hippocampus, and WMH were assessed. Extreme outlying data points (further than ±4 standard deviations [SD] from the mean) were excluded (0.002% of the total imaging-derived phenotype data analyzed). All MRI parameters were converted to z-scores, and WMH volume was log-transformed due to its skewed distribution.

Wang S., Wang J., Guo J., Dove A., Xu H., Qi X, & Xu W. (2023). Association of Kidney Function With Dementia and Structural Brain Differences: A Large Population-Based Cohort Study. The Journals of Gerontology Series A: Biological Sciences and Medical Sciences, 79(1), glad192.

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Comprehensive Brain Imaging Protocol

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Each participant was scanned using a Siemens Skyra 3 T scanner equipped with a 64-channel head/neck coil at the Pacific Radiology imaging centre in Dunedin, New Zealand. High-resolution structural images were obtained using a T₁-weighted MP-RAGE sequence with the following parameters: Repetition Time (TR) = 2400 ms; Echo Time (TE) = 1.98 ms; 208 sagittal slices; flip angle = 9°; Field of View (FOV) = 224 mm; matrix = 256 × 256; slice thickness = 0.9 mm with no gap (voxel size 0.9 mm × 0.875 mm × 0.875 mm); and total scan time = 6 min and 52 s. 3D FLAIR images were obtained with the following parameters: TR = 8000 ms; TE = 399 ms; 160 sagittal slices; FOV = 240 mm; matrix = 232 × 256; slice thickness = 1.2 mm (voxel size 0.9 mm × 0.9 mm × 1.2 mm); and total scan time = 5 min and 38 s.

d’Arbeloff T., Elliott M.L., Knodt A.R., Melzer T.R., Keenan R., Ireland D., Ramrakha S., Poulton R., Anderson T., Caspi A., Moffitt T.E, & Hariri A.R. (2019). White matter hyperintensities are common in midlife and already associated with cognitive decline. Brain Communications, 1(1), fcz041.

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Minimally Processed dMRI Data from the HCP1200

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Minimally pre-processed dMRI data, as described in Glasser et al. (2013) (link), from the HCP1200 release of the Human Connectome Project (HCP) (Van Essen et al., 2013 (link)) of 100 unrelated subjects (46 male, 54 female; aged 22–35), here-on defined as HCPUR100, was used to first create a clustered tractography template. Structural T1w data of these subjects were also used to create an anatomical template for cortical parcellation and lobular assignment lobes via FreeSurfer (Fischl et al., 2004 (link)). dMRI data was acquired on a customized Siemens Skyra 3T scanner (Van Essen et al., 2012 (link); Sotiropoulos et al., 2013 (link)) with the following scanning parameters: repetition time/echo time (TR/TE) = 5520/89.50 ms; resolution = 1.25 × 1.25 ×1.25 mm³; b-values = 1,000, 2,000, 3,000 s/mm² (90 directions each) with 18 b-value = 0 s/mm² images. Full acquisition details can be found in the HCP1200 subject reference manual.³

Kai J, & Khan A.R. (2022). Assessing the Reliability of Template-Based Clustering for Tractography in Healthy Human Adults. Frontiers in Neuroinformatics, 16, 777853.

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Mesial Prefrontal Cortex Functional Connectivity

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In Study 1, seed to whole brain intrinsic rsFC was examined for the mesial PFC (SMA, pre-SMA and dMPFC) and the mid-cingulate. For intrinsic baseline mapping, blood-oxygenation level dependent (BOLD) fMRI data was collected during rest (10 min, eyes open, watching white fixation cross on black screen) from 154 healthy volunteers (71 females; age 31 ± 13 years) at the Wolfson Brain Imaging Center, University of Cambridge, UK, with a Siemens Tim Trio 3T scanner and 32-channel head coil.
In Study 2, we used inhibitory, 1 Hz rTMS deep wide-field stimulation with an H7-coil targeting the mesial PFC. In order to examine the effects of rTMS on neural fluctuations, we used both ROI-to-ROI analyses and confirmed findings with independent component analysis (ICA). Resting state fMRI data (10 min, eyes open, watching white fixation cross) was collected immediately before and after rTMS (average time between rTMS end and EPI sequence was 285 ± 27 s) in a separate group of 20 healthy volunteers (15 females; age 36 ± 12 years) at the National Institutes of Health (Bethesda, MD, USA) core fMRI Facility, with a Siemens Skyra 3T scanner and 32-channel head coil.
All subjects provided informed written consent. This study was approved by the Research Ethics Committee of the University of Cambridge and the Institutional Review Board of the National Institutes of Health.

Popa T., Morris L.S., Hunt R., Deng Z.D., Horovitz S., Mente K., Shitara H., Baek K., Hallett M, & Voon V. (2019). Modulation of Resting Connectivity Between the Mesial Frontal Cortex and Basal Ganglia. Frontiers in Neurology, 10, 587.

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Neuroimaging Protocol for Brain Connectivity

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Each study member was scanned using a Siemens Skyra 3T scanner equipped with a 64-channel head/neck coil at the Pacific Radiology imaging center in Dunedin, New Zealand. Diffusion-weighted images providing full brain coverage were acquired with 2.5 mm isotropic resolution and 64 diffusion weighted directions (4700 ms repetition time, 110.0 ms echo time, b value 3,000 s/mm2, 240 mm field of view, 96×96 acquisition matrix, slice thickness = 2.5 mm). Non-weighted (b = 0) images were acquired in both the encoding (AP) and reverse encoding (PA) directions to allow for EPI distortion correction. High resolution structural images were obtained using a T1-weighted MP-RAGE sequence with the following parameters: TR = 2400 ms; TE = 1.98 ms; 208 sagittal slices; flip angle, 9°; FOV, 224 mm; matrix = 256×256; slice thickness = 0.9 mm with no gap (voxel size 0.9×0.875×0.875 mm); and total scan time = 6 min and 52 s. All neuroimaging data were visually inspected for quality. Data were excluded for Study members who were unable to be scanned with the 64-channel head coil, had an incidental finding, or whose scans were of poor quality due to motion (as revealed by visual inspection for T1-weighted images or >3 mm frame-to-frame movements for diffusion images), resulting in a total of 854 study members eligible for diffusion analyses and 860 study members eligible for GMV analyses.

Romer A.L., Knodt A.R., Sison M.L., Ireland D., Houts R., Ramrakha S., Poulton R., Keenan R., Melzer T.R., Moffitt T.E., Caspi A, & Hariri A.R. (2019). Replicability of structural brain alterations associated with general psychopathology: evidence from a population-representative birth cohort. Molecular Psychiatry, 26(8), 3839-3846.

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Longitudinal Brain Imaging in 3T MRI

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At baseline, scanning was performed in a Siemens Allegra 3-Tesla, head-only MRI scanner (Allegra Siemens Medical System, Malvern, PA, USA). High-resolution structure MRI sequences (FOV = 256 × 256 mm2, 256 × 256 matrix, thickness = 1.0 mm) were acquired. Follow-up scans were primarily performed on the Allegra (93%), but 4 of the 60 participants were scanned with a Siemens Skyra 3T scanner (MP-RAGE with a TR/TE of 2100ms/ 2.4ms, flip angle of 15°, TI of 1100ms, matrix size of 256x256, FOV of 22cm, slice thickness of 1mm).

Yokum S, & Stice E. (2016). Initial Body Fat Gain is related to Brain Volume Changes in Adolescents: a Repeated-Measures Voxel Based Morphometry Study. Obesity (Silver Spring, Md.), 25(2), 401-407.

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Healthy Participant Neuroimaging Data

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We used data from the HCP database (http://www.humanconnectome.org) derived from 823 healthy participants (462 women) with a mean age of 29 years (range 22–37 years). All neuroimaging data were acquired on a Siemens Skyra 3T scanner and preprocessed following standard HCP protocols^{31 (link)}. All the subjects provided informed consent^{32 (link)}. This study was approved by the institutional review board of the Icahn School of Medicine at Mount Sinai.

Moser D.A., Doucet G.E., Ing A., Dima D., Schumann G., Bilder R.M, & Frangou S. (2017). An integrated brain-behavior model for working memory. Molecular psychiatry, 23(10), 1974-1980.

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Resting-State fMRI and Structural MRI Acquisition

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Five minute, eyes-open resting state fMRI were acquired at the ONRC using a simultaneous multislice EPI sequence with factor of 8 from a Siemens Skyra 3T scanner with 32 surface coils. Both functional MRI and structural MRI were acquired axially paralleled with the AC-PC line with a whole-brain coverage. Functional MRI parameters were: FOV=240mm, flip angle = 60°; TR/TE = 475/30 ms; 49 slices; image matrix= 560× 560 × 49, voxel size = 3 × 3 ×3mm³. Twenty dummy volumes were discarded. Five MPRAGE images were also acquired axially paralleled with the AC-PC line with TE=2.88ms, flip angle = 13°, matrix size of 220 × 320 ×208, voxel size =0.8×0.8×0.8mm³. Subjects were asked to fixate on a cross sign in the center of the screen. They were instructed not to think of anything in particular and not to fall asleep.

Steffens D.C., Wang L., Manning K.J, & Pearlson G.D. (2017). Negative affectivity, aging, and depression: results from the Neurobiology of Late-life Depression (NBOLD) study. The American journal of geriatric psychiatry : official journal of the American Association for Geriatric Psychiatry, 25(10), 1135-1149.

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Multimodal Neuroimaging of Healthy Adults

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The neuroimaging data of healthy young adults (WU-Minn HCP open Data, HCP S1200 release), including structural MRI (T1-weighted image), diffusion MRI (dMRI), and resting-stage fMRI (rs-fMRI), were publicly obtained from the Human Connectome Project (HCP) database ConnectomeDB (https://www.humanconnectome.org)^{27 (link)}. The 33 healthy young adult unrelated subjects’ data were analyzed in the present study from the HCP database.
The HCP consortium has developed a common MRI acquisition protocol in the HCP reference manual (https://humanconnectome.org/storage/app/media/documentation/s1200/HCP_S1200_Release_Reference_Manual.pdf). Briefly, Siemens Skyra 3T scanner was used to acquire multi-modal MRI data^{28 (link)}. The structural data (T1-weighted image) consisted of one 0.7 mm isotropic scan in each subject. For dMRI, data was acquired with a spatial resolution (1.25 mm isotropic), multiple angular contrasts (b = 1000, b = 2000, and b = 3000 s/mm²), and high SNR (multiple averages and dense sampling in q-space, giving 570 volumes). For rs-fMRI, total of 4 fMRI runs were acquired in 2 mm isotropic resolution with a TR of 0.72 s for each 15 min period. Then, HCP MRI data were preprocessed by a common automated preprocessing framework^{29 (link)}.

Jitsuishi T, & Yamaguchi A. (2023). Characteristic cortico-cortical connection profile of human precuneus revealed by probabilistic tractography. Scientific Reports, 13, 1936.

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Multimodal MRI Acquisition Protocol

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Preoperative MRI data were acquired on a Siemens Skyra 3T scanner (Erlangen, Germany) equipped with a 32-channel receiver head coil at Charité University Hospital, Berlin, Department of Neuroradiology. These data consisted of a high-resolution contrast enhanced T1-weighted structural scan (TR/TE/TI 2300/2.32/900 ms, 9° flip angle, 256 × 256 matrix, 1 mm isotropic voxels, 192 slices, acquisition time: 5 min) and a single shell dMRI 2 × 2 × 2 mm³ voxels, 128 × 128 matrix, 60 slices, 3 b0 volumes) image data set, acquired at b = 0 and 1000 s/mm² with 5 and 30 volumes respectively, for a total acquisition time of 12 min. Additionally, T2-weighted and 3D fluid-attenuated inversion recovery (FLAIR) and subtraction sequences were performed.

Fekonja L.S., Wang Z., Cacciola A., Roine T., Aydogan D.B., Mewes D., Vellmer S., Vajkoczy P, & Picht T. (2022). Network analysis shows decreased ipsilesional structural connectivity in glioma patients. Communications Biology, 5, 258.

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