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246 protocols using prisma scanner

1

Preprocessing High-Density EEG Data

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Due to the timing errors in the EPI and MB-EPI pulse sequences on the Prisma scanner and in the EGI acquisition software, which resulted in failure of gradient artefact removal, it was not possible to assess the data quality of the high-density 256 channel EEG array implemented in the Siemens Prisma scanner.
The EEG data acquired with the 64-channel BrainCapMR equipment on the Philips Achieva scanner were preprocessed using BrainAnalyzer 2.0 (Brain Products GmbH, Gilching, Germany). These steps included gradient artifact removal using the sliding window approach with 21 averages [19 (link)], down-sampling from 5kHz to 500 Hz and correction of BCG using the sliding window approach. Data with evident noise after visual inspection were additionally run through an ICA where noise components were removed before a back-projection was applied (BrainAnalyzer 2.0).
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2

Resting-State fMRI Preprocessing Pipeline

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A 3T Siemens PRISMA scanner (Siemens Healthineers) was used to obtain BOLD fMRI data through use of Human Connectome Project sequences (multiband factor = 8, repetition time = 800 ms, echo time = 37, fractional anisotropy = 52°, field of view = 200 × 200, 72 slices, 2 mm isotropic voxels). Standard preprocessing steps were applied in Analysis of Functional NeuroImages (AFNI) consistent with the afni_proc.py pipeline, as described in previous publications (36 (link)). Briefly, preprocessing steps included slice timing correction, motion correction, spatial distortion correction, cross-registration to a magnetization prepared rapid acquisition gradient-echo structural scan, warping to the Montreal Neurological Institute-27 template, and smoothing (6 mm full width at half maximum). For single-subject analyses, regression models (using AFNI’s 3dDeconvolve) included motion parameters and their derivatives and were utilized to generate resting-state whole brain maps. The fast ANATICOR tool was used to reduce white matter artifacts. Bandpass filtering (0.01 < f < 0.1 Hz) was done through inclusion of a bandpass regressor in regression models.
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3

Preprocessing of Resting-State fMRI Data

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A 3T Siemens PRISMA scanner (Siemens Healthineers) was used to obtain BOLD fMRI data through use of Human Connectome Project sequences (multiband factor = 8, repetition time = 800 ms, echo time = 37, fractional anisotropy = 52°, field of view = 200 × 200, 72 slices, 2 mm isotropic voxels). Standard preprocessing steps were applied in Analysis of Functional NeuroImages (AFNI) consistent with the afni_proc.py pipeline, as described in previous publications (36 (link)). Briefly, preprocessing steps included slice timing correction, motion correction, spatial distortion correction, cross-registration to a magnetization prepared rapid acquisition gradient-echo structural scan, warping to the Montreal Neurological Institute-27 template, and smoothing (6 mm full width at half maximum). For single-subject analyses, regression models (using AFNI’s 3dDeconvolve) included motion parameters and their derivatives and were utilized to generate resting-state whole brain maps. The fast ANATICOR tool was used to reduce white matter artifacts. Bandpass filtering (0.01 < f < 0.1 Hz) was done through inclusion of a bandpass regressor in regression models.
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4

Alcohol Cue-Reactivity Neuroimaging Protocol

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Participants were scanned at the midpoint study visit (Day 8). Neuroimaging took place at the UCLA Center for Cognitive Neuroscience on a 3.0 T Siemens Prisma Scanner (Siemens Medical Solutions USA, Inc., Malvern, PA). Detailed neuroimaging procedures can be found in the Supplement. Participants completed a 720-s-long alcohol cue-reactivity task [40 (link)], in which they were presented with 24 pseudo-randomly interspersed blocks of alcoholic beverage images (ALC), non-alcoholic beverage images (BEV), blurred images to serve as visual controls, and a fixation cross. Each block was composed of five individual pictures of the same type, each presented for 4.8 s, for a total of 24 s. Each block was followed by a 6-s washout period during which participants reported on the urge to drink. Alcoholic beverage blocks were distributed between images of beer, wine, and liquor (two of each).
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5

Neuroimaging Analysis of Alcohol Cue Reactivity

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Neuroimaging for both studies took place at the UCLA Center for Cognitive Neuroscience on a 3.0 T Siemens Prisma Scanner (Siemens Medical Solutions USA, Inc., Malvern, PA). The neuroimaging visit took place on study day 10–14 for Study 1 and on study day 8 for Study 2. A T2-weighted, high-resolution matched-bandwidth (MBW) anatomical scan (time to repetition (TR) = 5000 ms, time to echo (TE) =34 ms, flip angle = 90°, voxel size: 1.5 mm × 1.5 mm × 4 mm, field of view (FOV) = 192 mm2, 34 slices, ~1.5 min) and a T1-weighted magnetization-prepared rapid gradient-echo (MPRAGE) sequence (TR = 2530 ms, TE =1.74 ms, time to inversion = 1260 ms, flip angle = 7°, voxel size: 1 mm3, FOV = 256 mm2, ~6.2 min) were acquired for co-registration to the functional data. A T2*-weighted echo planar imaging (EPI) scan (TR = 2200 ms, TE =35 ms, flip angle = 90°, FOV = 192 mm, slices = 36, 3.0 mm, ~12 min) was acquired to examine the blood oxygen-level dependent (BOLD) signal during the alcohol cue reactivity task.
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6

Comparative MRI Imaging of Abdominal and Pelvic Regions

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All subjects underwent MR imaging of the abdomen and pelvis. For the Asian cohort, images were acquired at the Clinical Imaging Research Centre (CIRC), Yong Loo Lin School of Medicine, NUS, in a 3T Siemens Prisma scanner (Siemens Healthineers, Erlangen, Germany). Participants were scanned in the supine position and two stacks of axial two-echo Dixon images with 2 mm slice thickness were acquired, covering the abdomen and the pelvis. The acquisition time per stack was 1 min and 56 s. The Caucasian cohort underwent MRI scanning at the Department of Diagnostic and Interventional Radiology, Klinikum Rechts der Isar, School of Medicine, Technical University of Munich, in a 3T Philips Ingenia scanner (Philips Healthcare, Best, The Netherlands). Two stacks of axial two-echo Dixon 3D spoiled gradient-echo images with 5 mm slice thickness were acquired, covering the abdomen and the pelvis. The acquisition time for each two-echo Dixon sequence was 10.6 s and each scan was performed in a single breath-hold (Table 1).
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7

Resting-state fMRI and Structural MRI Acquisition

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MRI data of all subjects were acquired on a 3.0 T Siemens Prisma scanner (Siemens AG, Healthcare Sector) using a 64-channel head coil. Each subject was required to keep in the supine position by a belt and foam pads during rest and awake condition with eyes closed. fMRI data was scanned using a gradient-echo echo-planer imaging (EPI) sequence of 240 volumes in an ascending interleaved order using the following protocols: repetition time (TR)/echo time (TE) = 2,000/40 ms, flip angle = 90°, field of view (FOV) = 240 mm × 240 mm, slice thickness = 4.0 mm, inplane resolution = 64 × 64, 32 axial slices with a slice gap of 1 mm. Then, high-resolution brain structural images were collected with a T1-weighted 3D magnetization-prepared rapid gradient-echo (MPRAGE) sequence (TR/TE = 1,900 ms/2.26 ms, matrix = 240 × 256, FOV = 215 mm × 230 mm, slice thickness/gap = 1.0/0 mm, 176 sagittal slices).
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8

Comparative Analysis of Primate Diffusion MRI

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This study evaluates variability in diffusion-weighted measurements across sites available in the PRIME-DE project, as well as between human MRI scanner models and vendors used to acquire the images. From the 25 sites in the database, 8 gathered diffusion data, and only 4 have a fair number of subjects (N ≥ 4): Aix-Marseille University (Aix-Marseille, 4 subjects, Siemens Prisma scanner), University of California, Davis (UC-Davis, 19 subjects, Siemens Skyra scanner), Mount Sinai School of Medicine—Philips (Sinai-Philips, 9 subjects, Philips Achieva scanner), and Siemens (Sinai-Siemens, 6 subjects, Siemens Skyra scanner). All subjects are Macaca Mulatta primates, anesthetized before acquisition. The scan sequence parameters can be found in Table 1. All datasets were acquired using 3T systems, with DWI at spatial resolutions from 0.7 to 1.4 mm3–isotropic or rectangular voxels—and anatomical images from 0.3 to 0.8 mm3 isotropic voxels.
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9

Resting-State fMRI Before and After Ketamine Intervention

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Scanning took place before the first ketamine infusion and one day after the 6th ketamine infusion. All neuroimaging data for the study were acquired using a 3T Siemens Prisma scanner at the Center for Magnetic Resonance Research at UMN. We utilized a multiband echo planar imaging sequence to improve the spatial and temporal resolution of the acquired fMRI data over conventional methods (Feinberg et al., 2010 (link)). Individual rs-fMRI data (eyes open, fixation cross, multiband factor of 8, time repeat of 710 ms, echo time of 30 ms, 2 mm isotropic voxel size, 680 volumes (~8 min)), along with a B0 field map and high resolution T1-weighted magnetization-prepared rapid acquisition with gradient echo anatomical scan (time repeat of 2530 ms, echo time of 3.65 ms, inversion time of 1100 ms, 7 degree flip angle, 1 mm isotropic voxel size, 4 min), were collected before and after the ketamine intervention for all 13 study participants.
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10

High-resolution Neuroimaging of Brain Structure and Function

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All participants were scanned at the Dartmouth Brain Imaging Center using a 3 Tesla Siemens Prisma Scanner with a 32-channel head coil. Anatomical T1-weighted images were collected using a high-resolution 3D MP-RAGE sequence, with 160 contiguous 1-mm-thick slices (TE =4.6 ms, TR =9800 ms, FOV=240 mm, flip angle=8°, voxel size=1 x 0.94 x 0.94 mm). Functional images were acquired using an echo-planar T2*-weighted imaging (EPI) sequence. Each volume consisted of 54 slices with 135 mm coverage (TE=31 ms, TR=2500 ms, flip angle=79°, voxel size = 2.5 x 2.5 x 2.5mm, PAT=2, Grappa=1, SMS=2).
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