Connectome scanner

Manufactured by Siemens

The Connectome scanner is a specialized medical imaging device designed for high-resolution mapping of the brain's neural connections. It utilizes advanced magnetic resonance imaging (MRI) technology to capture detailed images of the brain's intricate network of neurons and their interconnections. The Connectome scanner's core function is to provide researchers and clinicians with comprehensive data on the structural and functional connectivity of the human brain.

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Lab products found in correlation

Prisma scanner, by Siemens (1 mentions) Connectome skyra, by Siemens (1 mentions) 3t connectome skyra, by Siemens (1 mentions)

5 protocols using connectome scanner

Multimodal Neuroimaging Data Acquisition Protocols

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The HCP data were collected from a customized 3T Siemens Connectome scanner equipped with a 32-channel head coil. BOLD images were acquired using a multiband GRE-EPI sequence with the following parameters: TR = 720 ms, TE = 33.1 ms, FA = 52°, FOV = 208 × 180 mm², 2 mm slice thickness, 72 slices, multiband factor = 8. Of note, unlike the commonly applied phase-encoding directions along the “anterior-posterior” axis, the HCP fMRI data were acquired using left-right and right-left phase-encoding directions to accelerate scan time and to minimize image distortion^{11 (link)}. Each paradigm was scanned with two sessions, with each direction per session. In addition, T1-weighted and T2-weighted images were acquired using 3D-MPRAGE and 3D-T2-SPACE sequences with 0.7 mm voxel size and 224 × 224 mm² FOV. The T1 images used a TR of 2400 ms and TE of 2.14 ms, and the T2 images used a TR of 3200 ms and TE of 565 ms.
The STAR data were acquired from a 1.5 T GE scanner equipped with a standard 8-channel head coil. GRE-EPI sequence was used for functional imaging: TR = 2500 ms, TE = 40 ms, FA = 90°, 3.5 mm slice thickness, voxel size 3.44 × 3.44 × 4.5 mm³. T2-weighted images were scanned using a spin-echo sequence with 4000 ms TR, 82 ms TE, and 4 mm slice thickness.

Cao H., Ingvar M., Hultman C.M, & Cannon T. (2019). Evidence for cerebello-thalamo-cortical hyperconnectivity as a heritable trait for schizophrenia. Translational Psychiatry, 9, 192.

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Human Connectome Project: Comprehensive MRI Protocol

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The Human Connectome Project Young Adult (Van Essen et al., 2012 (link)) is a cross-sectional study including 3T MRIs from 1200 healthy participants acquired on a customized Siemens scanner (Connectome Skyra). It provides 0.7 mm isotropic de-faced scans of individuals between ages 22 and 35. All scans follow the same MPRAGE protocol with TR 2.4 s, TE 2.14 ms, TI 1 s, and flip angle of 8°. The full dataset is available online.⁴ The Human Connectome Lifespan Pilot Project (Phase 1a)⁵ is an extension of the Young Adult project and contains imaging data from five age groups. Five participants per age group 25–35, 45–55, and 65–75 were scanned on a 3T Siemens Connectome scanner at an isotropic voxel resolution of 0.8 mm following the Young Adult protocol except for a slightly smaller TE of 2.12 ms. In the present study, 30 cases from the Young Adult dataset are used for network training and 20 for validation. A total of 80 cases are used in the final test set. Further, 10 scans from the Lifespan Pilot Project are assembled into a separate test set to assess generalizability to another dataset at 0.8 mm in Section 4.4.

Henschel L., Kügler D, & Reuter M. (2022). FastSurferVINN: Building resolution-independence into deep learning segmentation methods—A solution for HighRes brain MRI. NeuroImage, 251, 118933.

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Multimodal MRI Data Acquisition Protocols

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Among multimodal MRI data acquired for the HCP‐YA, HCP‐D, and HCP‐A, T2‐ and T1‐weighted structural MRI data collected on 3 T scanners (customized Connectome scanner for the HCP‐YA; standard Siemens Prisma scanner for the HCP‐D and HCP‐A) were employed in this study. T2‐weighted and T1‐weighted images were obtained with the 3D SPACE (Sampling Perfection with Application‐optimized Contrasts using different flip angle Evolution) sequence and with the 3D MPRAGE (Magnetization‐Prepared Rapid Acquisition with Gradient Echo) sequence, respectively, in sagittal slices at a submillimeter isotropic spatial resolution (0.7 mm isotropic voxels for the HCP‐YA; 0.8 mm isotropic voxels for the HCP‐D and HCP‐A). Details about imaging protocols for the HCP‐YA, HCP‐D, and HCP‐A can be found elsewhere (https://www.humanconnectome.org/).

Park C., Shin N., Nam Y., Yoon U., Ahn K, & Lee S. (2023). Characteristics of perivascular space dilatation in normal aging. Human Brain Mapping, 44(8), 3232-3240.

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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).

Grumbach P., Opel N., Martin S., Meinert S., Leehr E.J., Redlich R., Enneking V., Goltermann J., Baune B.T., Dannlowski U, & Repple J. (2020). Sleep duration is associated with white matter microstructure and cognitive performance in healthy adults. Human Brain Mapping, 41(15), 4397-4405.

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Multimodal MRI Acquisition Protocols

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2.2.1 DTD and HC2 databases. Participants were scanned using a 3T GE Discovery 750 MRI with an eight-channel head coil. Twenty-two individuals (DTD=9, HC2=13) were scanned in 2011 and 2013, and anatomical images were acquired using a T1-weighted SPGR sequence (Minimum Full TE, 11° flip angle, 1 mm isotropic voxels, 25.6 cm FOV). Sixteen additional individuals (DTD=11, HC2=5) were scanned in the same scanner in 2017, with anatomical images acquired using a T1-weighted fast SPGR sequence (Minimum Full TE, 10° flip angle, 1 mm isotropic voxels, 25.6 cm FOV, ARC factor 2). 2.2.2 HC1 database. All HC participants were scanned on a customized Siemens 3T "Connectome Skyra" housed at Washington University in St. Louis, using a standard 32-channel Siemens head coil and a body transmission coil designed by Siemens using the gradients of the WU-Minn and MGH-UCLA Connectome scanners. T1-weighted 3D MPRAGE were acquired with TR=2400 ms, TE=2.14 ms, TI=1000 ms, 8° flip angle, FOV=224x224, 0.7 mm isotropic voxel, bandwidth=210 Hz/px, iPAT=2, and acquisition time=7:40 (min:sec).

Fragueiro A., Cury C., Santacroce F., Burles F., Iaria G, & Committeri G. (2024). Medial positioning of the hippocampus and hippocampal fissure volume in developmental topographical disorientation. Hippocampus, 34(4).

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