MRI scans were conducted at the Children’s Hospital of Philadelphia on a research-dedicated 3T Siemens Verio system using a 32-channel head coil. All scans were carried out by a single operator and monitored to be free of artifacts at the time of acquisition. Details of image acquisition and processing for structural and functional neuroimaging are presented in the Supplementary Materials .
Verio system
Manufactured by Siemens
Sourced in Germany
The Verio system is a laboratory equipment product offered by Siemens. It is designed to provide core functionality for various laboratory applications. The description of its specific features and intended use is not available at this time.
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30 protocols using verio system
1
Structural and Functional Neuroimaging Using 3T MRI
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Fetal Brain MRI Using 3D-SWI Sequence
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Longitudinal Structural MRI in Neurosurgery
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Structural MRI was conducted within 1 week on average before surgery and postoperatively within 48 h after surgery or a pseudo surgery (for non-surgery peers) date. Participants were scanned at two different time points, one corresponding to before surgery and one corresponding to after surgery using a 3.0 T Siemens Verio system with an 8-channel head coil. T1-weighted and diffusion weighted MRI were acquired at both timepoints and T2 FLAIR acquired only at baseline.
T1-weighted images were acquired with the following parameters: TR: 2500 ms; TE: 3.77 ms; 176 sagittal 1 mm3 slices, 1 mm isotropic resolution; 256 × 256 × 176 matrix, 7/8 phase partial Fourier. Fluid attenuated inversion recovery (FLAIR) images were acquired with the following parameters: 176 contiguous slices, 1 mm3 voxels, TR/TE = 6000/395 ms. Diffusion weighted images were acquired with the following parameters: TR/TE = 17300/81 ms, two scans without diffusion weighting, six diffusion gradient directions with b-value of 100 s/mm2 and 64 diffusion gradient directions with b-value of 1000 s/mm2. The diffusion gradients were distributed following a scheme of electrostatic repulsion (Jones et al., 1999 (link)). The diffusion-weighted images covered the entire brain with an isotropic resolution of 2.0 mm, field of view (FOV) of 256 mm × 256 mm, and 73 slices.
T1-weighted images were acquired with the following parameters: TR: 2500 ms; TE: 3.77 ms; 176 sagittal 1 mm3 slices, 1 mm isotropic resolution; 256 × 256 × 176 matrix, 7/8 phase partial Fourier. Fluid attenuated inversion recovery (FLAIR) images were acquired with the following parameters: 176 contiguous slices, 1 mm3 voxels, TR/TE = 6000/395 ms. Diffusion weighted images were acquired with the following parameters: TR/TE = 17300/81 ms, two scans without diffusion weighting, six diffusion gradient directions with b-value of 100 s/mm2 and 64 diffusion gradient directions with b-value of 1000 s/mm2. The diffusion gradients were distributed following a scheme of electrostatic repulsion (Jones et al., 1999 (link)). The diffusion-weighted images covered the entire brain with an isotropic resolution of 2.0 mm, field of view (FOV) of 256 mm × 256 mm, and 73 slices.
4
MRI Imaging Protocol for Stem Cell Therapy
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Magnetic resonance imaging (MRI) was performed on a 3‐Tesla Verio system (Siemens Medical Systems, Erlangen, Germany). All patients underwent an MRI scanning at baseline (less than 72 hours prior to stem cell injection) then at 3, 6, and 12 months post‐MSCs injection. The detailed imaging sequences protocol of the brain and those of the cervical and thoracic spine can be found in Appendix S2 . T2‐weighted FLAIR and T1‐weighted MPRAGE images were generated for all patients.
The T2‐hyperintense lesion volume measurements were obtained using a semi‐automated segmentation technique based on Fuzzy connections algorithm in JIM software (Jim version 3; Xinapse Systems, Colchester, England).34
The T2‐hyperintense lesion volume measurements were obtained using a semi‐automated segmentation technique based on Fuzzy connections algorithm in JIM software (Jim version 3; Xinapse Systems, Colchester, England).
5
Resting-State fMRI Acquisition on 3T Siemens Verio
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MR images were acquired on a 3T Siemens Verio system (Siemens, Germany). All subjects were instructed to rest with their eyes closed, not to think about anything in particular, or to fall asleep. A gradient-recalled echo-planar imaging (GRE-EPI) pulse sequence was used for acquiring resting state functional images, with the parameters as follows: TR = 2000 ms, TE = 30 ms, flip angle = 90°; matrix size = 64 x 64, FOV = 220 x 220 mm2, thickness/gap = 3.5 mm/0.6 mm, in-plane resolution of 3.4 mm x 3.4 mm, slices numbers = 31. The scan for resting state fMRI lasted for 280 seconds, containing 140 brain volumes. Thereafter, anatomical images were acquired using a T1-FLAIR sequence, with the parameters as follows: TR = 2530 ms, TE = 3.34 ms, flip angle = 7°, matrix = 256 × 192, FOV = 256 x 256 mm2, thickness/gap = 1.33 mm/0.5 mm, slices numbers = 128.
6
Optimized fMRI Acquisition in Orbitofrontal Cortex
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MRI data were acquired on a 3 T Siemens Verio system equipped with a 32 channel phased array head coil (Siemens, Germany). First, a high-resolution T1-weighted scan was acquired using an MPRAGE sequence. For functional imaging, 45 slices with a voxel resolution of 3 mm isotropic were obtained (no gap) using a sequence optimized for the orbitofrontal cortex (Deichmann et al., 2003 (link)), with TR = 3000 ms, TE = 30 ms, flip angle = 87°, a slice angle of 15° and a local z-shim applied around the region of the orbitofrontal cortex. Field maps were acquired using a dual echo 2D gradient echo sequence with TR = 488 ms and TE of 7.65 ms and 5.19 ms on a 64 × 64 × 40 grid. A total of 881 volumes were acquired on average, depending on subjects' reaction times, thus resulting in a total task duration of about 44 min. We used Presentation (Neurobehavioural Systems, USA) to present the task and record subjects' behaviour.
7
Multiband fMRI and Structural MRI Protocol
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Multiband gradient echo EPI fMRI was conducted on a 3T Siemens Verio system using a 32-channel volume head coil (310 vol, TR = 2 s, TE = 29 ms, multiband factor = 3, FOV = 256 × 256 × 144 mm3, acquisition matrix = 128 × 128, 72 axial slices, pixel resolution = 2 × 2 × 2 mm3, 10:48 mts). A high-resolution (1 mm3) structural T1-weighted MRI image was also collected. A scout image in each plane was acquired followed by a 3D T1-weighted anatomical MRI image [3D Magnetization Prepared Rapid Gradient Echo (MPRAGE) sequence, TR = 2,150 ms, TE = 3.53 ms, TI-1,100 ms, flip-angle = 8°, FOV = 256 × 256 × 160 mm3, 160 axial slices of thickness = 1 mm, pixel resolution = 1 × 1 × 1 mm3, 4:59 mts].
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Gradient-Echo EPI fMRI Acquisition Protocol
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Siemens Verio 3T MRI Imaging Protocol
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All MRI experiments were performed using a Verio system (Siemens, Germany) with a standard 12-channel head matrix coil operating at 3 Tesla.
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3T MRI Scans of Research Participants
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