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Connectome skyra

Manufactured by Siemens
Sourced in Germany, United States

The Connectome Skyra is a high-performance magnetic resonance imaging (MRI) system designed for advanced neuroimaging research. It features a powerful magnetic field strength, enabling detailed visualization and analysis of the brain's intricate connections, known as the connectome. The Connectome Skyra provides researchers with the necessary tools to study the complex neural networks and their functions.

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30 protocols using connectome skyra

1

Functional MRI Data Acquisition Protocol

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fMRI BOLD-contrast time series data collection was performed using gradient echo EPI on 3T Siemens “Connectome Skyra” machines with a 32-channel head coil (TR: 720 ms, TE: 33.1 ms, FOV: 208x180 mm2, acquisition matrix: 104x90, 72 axial slices, voxel dimensions: 2x2x2 mm3). A 3D T1-weighted anatomical MRI image was also acquired for each participant (TR: 2400 ms, TI: 1000 ms, TE: 2.14 ms, flip angle: 8°, FOV: 224x224 mm2).
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2

Multimodal MRI Neuroimaging Protocol

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MRI data from the Human Connectome Project (http://www.humanconnectome.org/) were collected on a 3 T Siemens Connectome Skyra, including a T1-weighted MPRAGE structural scan, resting-state functional MRI and DTI using multiband acquisitions.
MRI data from a separate cohort of TBI patients and healthy control subjects, were acquired using a 3 T Siemens Magnetom Verio Syngo with a 32-channel head coil. Standard clinical MRI was collected. Resting-state functional MRI data were also acquired, alongside a high-resolution T1-weighted image and DTI (see Supplementary material for details on the acquisition parameters for both cohorts).
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3

Resting-state fMRI Acquisition and Analysis

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To examine reproducibility and perform additional analyses, we used data from the HCP, which were acquired on a customized Siemens 3 T “Connectome Skyra” using a 32-channel Siemens receive head coil. To minimize WM signal contamination from nearby GM, unprocessed fMRI data were used from 100 participants (age range: 22–35 years; 50 females). For each participant, BOLD resting state data were acquired using multiband gradient echo planar imaging. The following parameters were used for data acquisition: TR = 720 ms, TE = 33.1 ms, matrix size = 104 × 90, flip angle = 52°, FOV = 20.8 × 18.0 cm2, 72 axial slices each 2 mm thick with left-right encoding, and 1200 volumes. High resolution T1-weighted images were acquired using a 3D GE sequence (0.7 × 0.7 × 0.7 mm3 nominal resolution, TR/TE = 2400/2.14 ms, flip angle = 8°).
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4

Diffusion MRI Acquisition Protocol for HCP

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DTI data were available for n = 1,065 subjects. Data from all HCP participants was acquired on a customized Siemens 3T “Connectome Skyra” at Washington University by using a standard 32‐channel Siemens receive head coil and a “body” transmission coil. This was specifically designed by Siemens for the smaller space available using the special gradients of the WU‐Minn and MGH‐UCLA Connectome scanners (Van Essen et al., 2013).
A full diffusion MRI session includes six runs (each ~9 min and 50 s), representing three different gradient tables, with each table acquired once with right‐to‐left and left‐to‐right phase encoding polarities, respectively. Each gradient table includes ~90 diffusion weighting directions plus 6 b = 0 acquisitions distributed throughout each run. Diffusion weighting consisted of 3 shells of b = 1,000, 2000, and 3,000 s/mm2 interspersed with an approximately equal number of acquisitions on each shell within each run (Sequence: Spin‐echo EPI, TR 5520 ms, TE 89,5 ms, flip angle 78 deg, refocusing flip angle 160 deg, FOV 210 × 180 (RO × PE), matrix 168 × 144 (RO × PE), slice thickness 1.255 mm, 111 slices, 1.25 mm isotropic voxels, multiband factor 3, echo spacing 0.78 ms, BW 1488 Hz/Px, phase partial fourier 6/8, b‐values 1,000, 2000, 3,000 s/mm2).
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5

High-Resolution Brain Imaging Cohort

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We randomly sampled 30 young healthy participants from HCP S900 release (15 females; 15 males; 22–35 years old). Their T1w images were acquired with a Siemens Connectome Skyra 3 T scanner using a high-resolution MPRAGE sequence (TR = 2.4 s, TE = 2.14 ms, TI = 1 s, flip angle = 8°, FOV = 224 × 224, voxel size = 0.7 × 0.7 × 0.7 mm3). The local review board at Washington University in St. Louis approved all study procedures. Written informed consent was obtained from each participant before study enrollment.
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6

Multimodal MRI Acquisition for Resting-State and Anatomical Analysis

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Detailed description of MRI acquisition parameters can be found in the previous study (Glasser et al., 2013 (link)), in which the resting-state fMRI (rsfMRI) and the high-resolution structural MRI were used. The rsfMRI dataset was acquired with eyes open with relaxed fixation on a projected bright cross-hair on a dark background with following parameters: repetition time (TR) = 720 ms; echo time (TE) = 33.1 ms; flip angle = 52°; field of view (FOV) = 208 × 180 mm; image matrix = 104 × 90; 72 slices with 2 mm isotropic voxels; multiband factor = 8; number of runs = 4; scans per run = 1200; duration of each run = 14 min 33 sec). T1-weighted (T1w) and T2-weighted (T2w) structural MRIs were acquired for the anatomical reference (T1w: TR = 2.4 sec; TE = 2.14 ms; inversion time (TI) = 1 sec; FOV = 224 × 224; 0.7 mm isotropic voxels; T2w: TR = 3.2 sec; TE = 565 ms; FOV = 224 × 224; 0.7 mm isotropic voxels). All MRI data was acquired from a 3 T Siemens Connectome Skyra with a 32-channel head coil.
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7

HCP Resting-State fMRI Protocol

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The second data set used in this study was the resting‐state fMRI (rs‐fMRI) data from the “unrelated 100” subjects (54 female, 46 male adults, aged from 22 to 35), which was made publicly available in the HCP S1200 release (van Essen et al., 2013 (link)). The rs‐fMRI scans for each subject were collected in two sessions held on different days, including a total four runs of approximately 15 min each. During the scans, the subjects were asked to fixate a white cross‐hair on a dark background.
The HCP resting‐state fMRI time series were acquired using 3T Siemens “Connectome Skyra” scanner with 2 × 2 × 2 mm spatial resolution and a TR of approximately 0.7 s. For more details of the data acquisition parameters, see Smith et al. (2013 (link)) and Uğurbil et al. (2013 (link)).
All data were pre‐processed using the HCP minimal processing pipeline (Glasser et al., 2013 (link)), including structural registration, correction for spatial distortion, head motion, cortical surface mapping, and functional artifact removal (Glasser et al., 2013 (link); Smith et al., 2013 (link)). For each rs‐fMRI run, this resulted in 1200 time points for each of the 32k vertices of the standard fsLR‐32K template (van Essen et al., 2012 (link)) per hemisphere. To generate the functional profiles for the HCP data set, we concatenated all four runs after mean‐centering.
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8

Highly Detailed MRI Acquisition Protocol

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All MRI data were obtained at Washington University in St. Louis, MO, on a Siemens 3T MR scanner “Connectome Skyra,” which was customized with a 100mT/m gradient coil and inner bore diameter of 56 cm, using a standard 32‐channel head coil.
A 3D T1‐weighted Magnetization‐Prepared Rapid Acquisition with Gradient Echo (MPRAGE) sequence was acquired with the following parameters: sagittal acquisition with FOV = 224 × 224 × 180 mm; voxel size = 0.7 × 0.7 × 0.7 mm3; repetition time = 2,400 ms; echo time = 2.14 ms; inversion time = 1,000 ms; band width = 210 Hz/pixel; flip angle = 8°; GeneRalized Autocalibrating Partial Parallel Acquisition (GRAPPA) factor = 2; and total acquisition time = 7 min 40 s.
A 3D T2‐weighted Sampling Perfection with Application‐optimized Contrasts using different flip angle Evolution (SPACE) sequences was acquired with the following parameters: sagittal acquisition with field of view = 224 × 224 × 180 mm; voxel size = 0.7 × 0.7 × 0.7 mm3; repetition time = 3,200 ms; echo time = 565 ms; echo spacing = 3.53 ms; turbo factor = 314; echo train duration = 1,105 ms; band width = 744 Hz/pixel; variable flip angle; GRAPPA factor = 2; and total acquisition time = 8 min 24 s.
More detailed information regarding imaging protocols can be found in the WU‐Minn Human Connectome Project S1200 Release Reference Manual (Van Essen et al., 2013).
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9

High-Resolution MRI Imaging Pipeline

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Magnetic resonance imaging was done using a customized 3 T Siemens Connectome Skyra with a standard 32-channel Siemens receiver head coil and a body transmission coil. T1-weighted high-resolution structural images were acquired using a 3D MPRAGE sequence with 0.7 mm isotropic resolution (FOV = 224 × 224 mm, matrix = 320 × 320, 256 sagittal slices, TR = 2400 ms, TE = 2.14 ms, TI = 1000 ms, FA = 8°). T2-weighted high-resolution structural images were acquired using a 3D T2-SPACE sequence with 0.7 mm isotropic resolution (FOV = 224 × 224 mm, matrix = 320 × 320, 256 sagittal slices, TR = 3200 ms, TE = 565 ms). Images were pre-processed to correct for distortions introduced by gradient non-linearities, remove readout distortions, correct for bias field distortions and align the images to the MNI space template.
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10

Multimodal Neuroimaging of Brain Connectivity

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We used the unrelated subjects sample (n = 339, 156/183 m/f, ages 22–35) from the full release of the publicly available Human Connectome Project data set36 (link). In our prediction analysis, we excluded participants that had missing behavioural data in a case-by-case fashion (Table 1). The HCP scanning protocol was approved by the local Institutional Review Board of Washington University in St. Louis, MO, USA, and informed consent was obtained from all participants, the details of which are described elsewhere36 (link). In brief, for resting-state fMRI (rs-fMRI), whole-brain multiband gradient-echo-planar images were acquired on a 32-channel 3 T Siemens “Connectome Skyra” scanner with TR = 720 ms, TE = 33.1 ms, flip angle = 52 degrees, bandwidth = 2290 Hz/pixel, in-plane field of view = 208 × 180 mm2, 72 slices, 2 mm isotropic voxels and 1200 volumes (14 min and 24 s). Rs-fMRI sessions were acquired left-to-right (LR) and right-to-left (RL). Furthermore, there were two separate rs-fMRI sessions for each individual (“rest 1” and “rest 2”) acquired on two different days.
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