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48 protocols using trio 3.0 t scanner

1

Resting-state fMRI Acquisition for Schizophrenia and ASD

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Resting-state fMRI data for the schizophrenia dataset were acquired on a Siemens 3.0 T Trio scanner (Siemens Medical Systems, Erlangen, Germany), using an echo-planar imaging sequence with the following parameters: TR/TE = 2000/30 ms, flip angle = 90 degrees, 33 slices, acquire matrix = 64×64, field of view = 220×220 mm2, gap = 0.6 mm, voxel size = 3.4×3.4×4 mm3. 240 volumes resulting in 8 minutes of data were obtained.
Resting-state fMRI data for the ASD dataset were acquired on a Siemens 3.0 T Trio scanner (Siemens Medical Systems, Erlangen, Germany), using an echo-planar imaging sequence with the following parameters: TR/TE= 2000/25 ms, flip angle = 60 degrees, 34 slices, acquire matrix = 64×64, field of view = 220×220 mm2, no gap, voxel size = 3.4×3.4×4 mm3. 200 volumes resulting in 6.7 minutes of data were obtained.
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2

Resting-State fMRI Acquisition Protocol

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Head motion of more than 2.0 mm maximum displacement in any of the X, Y, or Z directions or 2.5 degrees of any angular motion were not included (see Data analysis). All images were acquired on a SIEMENS 3.0 T Trio scanner (Siemens Medical Solutions, Erlangen, Germany) in Huaxi MR Research Center, West China Hospital of Sichuan University (China). Foam pads were used to prevent head movement. Functional images were obtained using an echo-planar imaging sequence with the following parameters: 33 axial slices, thickness/gap = 3.0/0.6 mm, in-plane resolution = 64 × 64, repetition time = 2,000 ms, echo time = 30 ms, flip angle = 90°, field of view = 200 × 200 mm2. Participants who performed in the resting-state session were instructed to try to hold still, not think systematically, and not fall asleep.
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3

Functional MRI Acquisition Protocol

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Images were acquired with a Siemens Trio 3.0 T scanner in the Laboratory of Cognition and Personality in Southwest University (China). Functional data were acquired in an interlaced way along the AC–PC line with a T2-weighted EPI sequence of 24 axial slices (TR = 1500 ms, TE = 30 ms, flip angle = 90°, acquisition matrix = 64 × 64, thickness = 5 mm, inter-slice gap = 1 mm). Within each session, a total of 644 EPI images were acquired. At the end of the experiment, a T1-weighted spin echo data set (TR = 2000 ms, TE = 2.52 ms, flip angle = 90°, acquisition matrix = 256 × 256) was acquired.
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fMRI Protocol for Neuroimaging Analysis

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fMRI data were collected on a SIEMENS Trio 3.0 T scanner. Each subject lied on supine with the head in neutral position fixed comfortably by a belt and foam pads during the test. The scanning sessions included (1) localizer, (2) T1 MPRAGE anatomy (176 sagittal slices, thickness/gap = 1.0/0 mm, in-plane resolution = 256 × 256, FOV (field of view) = 240 mm × 240 mm, TR (repetition time) = 1,900 ms, TE (echo time) = 2.26 ms, and flip angle = 15°), (3) EPI-BOLD (36 axial slices, echo-planar imaging pulse sequence, thickness/gap = 5.0/1 mm, in-plane resolution = 64 × 64, TR = 3,000 ms, TE = 30 ms, flip angle = 90°, and FOV = 240 mm × 240 mm).
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5

Resting-State Brain Imaging Protocol

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All subjects underwent the resting‐state scanning on a TRIO 3.0 T scanner (Siemens Medical, Erlangen, Germany). Before scanning, participants were instructed to keep their eyes closed, stay relaxed, and remain physically still, but not to fall asleep. The whole scanning lasted 12 min, resulting in 360 volumes for each participant. The scanning parameters for functional images were as followed: TR = 2,000 ms; TE = 30 ms; flip angle = 90°; resolution matrix = 64 × 64; FOV = 200 × 200; slices = 33; voxel size = 3.1 × 3.1 × 3.6 mm3.
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6

Resting-state fMRI Acquisition and Analysis

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All subjects underwent resting-state functional magnetic resonance imaging (rs-fMRI). MR images were acquired on a Siemens Trio 3.0 T scanner (Siemens Medical Solutions, Erlangen, Germany). The resting-state paradigm was measured using a gradient echo planar imaging (EPI) sequence with the following parameters: TR = 2000 ms, TE = 30 ms, FOV = 220 mm, 32 slices, 3.4 × 3.4 × 3.4 mm3 voxel size, 1 mm gap, flip angle = 90°, rs-fMRI: 184 volumes (three dummy images). The slices covered the whole brain extending from the vertex to lower parts of the cerebellum.
For the resting-state assessment, subjects were instructed to remain motionless and to fixate on a red cross on a black screen for about 6 min. We choose a scanning time around 6 min because longer scanning times do not improve the signal-to-noise of the data, but promote fatigue of the subjects (Van Dijk et al., 2010 (link)).
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7

Volumetric MRI Analysis of Brain Structure

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Volumetric studies were based on magnetic resonance images acquired on a Siemens Trio 3.0-T scanner at the University of Utah. A 12-channel RF head coil was used to obtain 3D T1-weighted image volumes with 1-mm isotropic resolution using an MP-RAGE sequence (TI = 900 msec, TR = 2300 msec, TE = 2.91 msec, flip angle = 9°, sagittal, field of view = 25.6 cm, matrix = 256 × 256 × 160).
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8

Neuroimaging Protocol for Brain Mapping

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Data were acquired using a SIEMENS Trio 3.0 T scanner in the Beijing Normal University Imaging Center for Brain Research. fMRI data were obtained using an EPI sequence with the following parameters: TR = 2000 ms; TE = 25 ms; flip angle = 90°; 64 × 64 matrix size with a resolution of 3 × 3 mm2. Forty-one 3.0 mm axial slices were used to cover the whole cerebrum and most of the cerebellum with no gap. The slices were tilted 30 degrees clockwise from the AC-PC plane to obtain better signals in the orbitofrontal cortex. A high-resolution, T1-weighted sagittal 3-D magnetization prepared rapid gradient-echo sequence was acquired: TR = 2530 ms; TE = 3.39 ms; TI = 1100 ms; FA = 7°; FOV = 256 × 256 mm. 144 slices contiguous sagittal slices were acquired with 1 × 1 mm in-plane resolution and 1.33 mm slab thickness for whole brain coverage.
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9

MRI-Based Brain Tumor Segmentation

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MRI scans were performed using a Trio 3.0-T scanner (Siemens, Erlangen, Germany) to obtain the MR images and typically included axial T1WI (TE, 15 ms; TR, 450 ms; slice thickness, 5 mm), T2WI (TE, 110 ms; TR 5800 ms; slice thickness, 5 mm), and CE scans using 0.1 mM/kg gadopentetate dimeglumine (Ga-DTPA injection, Beilu Pharma, Beijing, China) (TE, 15 ms; TR, 450 ms; slice thickness, 5 mm), with field of view 240 × 188 mm2. The tumor masks were manually segmented on T2WI by two experienced neurosurgeons (ZF and SF >5 years of experience in diagnosis) using MRIcro software (http://www.mccauslandcenter.sc.edu/mricro/), and a third senior neuroradiologist (SL, >20 years of experience) reevaluated the tumor masks and made the final decision when discrepancies were >5%.
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10

Contrast Enhancement Evaluation of Glioma MRI

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The Cancer Genome Atlas MR images of AGs were downloaded from the Cancer Imaging Archive (TCIA, http://www.cancerimagingarchive.net). CGGA MR images of AGs were obtained from the CGGA imaging database ( http://www.cgga.org.cn) administered by the Chinese Glioma Cooperation Group. MR images in CGGA patients were generally obtained with a Trio 3.0T scanner (Siemens, Erlangen, Germany). Tumor CE was defined as newly emerged, unequivocally increased signal intensity on the T1‐weighted image following intravenous contrast administration when compared to noncontrast T1 images. Nonenhancement (nCE) was defined as no apparent enhancement in tumors on postcontrast T1‐weighted images, compared with regular T1‐weighted images (Figure 1). The presentation of tumor CE was evaluated by two experienced neuroradiologists (X.C. and J.M., both with more than 15 years of neuroradiological experiences) blinded to the patients‧ clinical information. A third senior neuroradiologist (S.L. with more than 20 years of neuroradiological experiences) arbitrated when necessary.
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