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160 protocols using 3t scanner

1

Healthy Brain MRI Diffusion Datasets

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MRI datasets of 10 healthy volunteers in the age range of 22–35 (6 female, 4 male) were obtained from the HCP Wu-Minn database (https://db.humanconnectome.org). Only non-restricted, anonymized open access datasets were used. Therefore, no ethical consent is necessary according to national laws and regulations. Subjects were scanned at a Siemens 3T scanner equipped with a dedicated, high performance gradient system capable of gradient strengths of 100 mT/m with special gradient amplifiers (Ugurbil et al., 2013 (link)). Three shells with b-values of 1,000, 2,000, and 3,000 s/mm2 were acquired with 90 diffusion encoding directions on each shell. The spatial resolution was 1.25 mm isotropic. Two phase-encoding direction reversed images for each diffusion direction were acquired. The non-diffusion weighted volumes with b = 0 were interleaved with DW volumes such that every sixteenth volume had no diffusion weighting. More details about the acquisition protocol can be found in Sotiropoulos et al. (2013 (link)).
The utilized diffusion datasets were already preprocessed by the HCP diffusion pipeline (Glasser et al., 2013 (link)). Briefly, distortions were corrected using a model-based approach that simultaneously takes into account susceptibility and eddy-current induced distortions, as well as head motion.
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2

Resting-State fMRI Acquisition Protocol

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A total of 250 resting-state volumes were acquired on a Siemens 3-T scanner. Participants were directed to lie still with their eyes closed and remain awake. Foam pads and soft earplugs were provided to attenuate head movement and scanner noise. The following parameters using a gradient-echo echo-planar imaging (EPI) sequence were applied in image acquisition: repetition time/echo time = 2000 ms/30 ms, 30 slices, 64 × 64 matrix, 90° flip angle, 24 cm field of view, 4 mm slice thickness, 0.4 mm gap, and the scan lasted for 500 seconds.
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Fast Spin Echo MRI Head Imaging

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The in vivo head dataset is an axial 2D fast spin echo dataset acquired on a 3T scanner (Siemens Healthineers, Erlangen, Germany) with 12 receive channels, 91 ms TE, 6000 ms TR, echo train length of 11, 195 × 220 mm FOV, and 286 × 320 acquisition matrix. The 12 coil channels were reduced to 4 channels with Siemens coil compression. Multiple slices were acquired at slice thicknesses of 1 mm and 2 mm. The phase encode lines were retrospectively undersampled at 4× and 6× acceleration using a one-dimensional (1D) variable density Poisson disc sampling with the central 24 lines fully sampled. This dataset was processed in the same manner as the in vivo knee dataset above.
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4

Working Memory fMRI in Alzheimer's

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All participants underwent pre- and post-intervention fMRI on a Siemens 3T scanner. While undergoing fMRI, participants performed a five-digit span working memory task adapted for people with Alzheimer's disease from a previous fMRI study in young healthy individuals,15 (link) requiring them to encode, retain and then verbally recall the five digits in order. Three blocks of twenty trials were performed and structured or random span sequences were presented pseudo-randomly. See online supplement DS1 for details of fMRI acquisition and analysis.
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5

MEG Recordings of Brain Activity

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Before entering the MEG shielded room, subjects were trained on the task. Participants were tested supine and MEG data were recorded continuously (600 Hz sampling rate, DC-100 bandpass) on a 151-channel whole-head CTF MEG (MISL, Coquitlam, BC, Canada). A T1-sagittal MPRAGE structural MR was obtained on a 3 T scanner (Siemens AG, Erlangen Germany) to allow co-registration of the MEG data to each subject's own brain anatomy.
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6

3T MRI Brain Scanning Protocol

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MRI brain scanning was performed on a 3T scanner (Siemens Medical, Erlangen, Germany): T1-weighted (T1-w) multiecho magnetization-prepared gradient echo (repetition time 2,530 milliseconds, inversion time 1,100 milliseconds, voxel size 1.0 mm3 isotropic) and T2-weighted (T2-w; repetition time 3,200 milliseconds, echo time 454 milliseconds, voxel size 1.0 mm3 isotropic) scans.
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7

Resting-State fMRI Acquisition Protocol

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All participants were scanned using a Siemens 3 T scanner housed at Washington University in St Louis. Scans were taken using a standard 32-channel Siemens receive head coil and a “body” transmission coil. The rsfMRI data were of approximately 15 minutes duration with eyes open and relaxed fixation on a projected bright crosshair on a dark background (in a dark room).
The structural and functional MRI images were acquired using the following parameters [48 (link)]:
Structural MRI: T1w 3D magnetization-prepared rapid acquisition with gradient echo (MPRAGE), Field of View: 224 × 224 mm, TR = 2400 ms, TE = 2.14 ms, Flip Angle= 8, Voxel size= 0.7 mm isotropic. T2W 3D T2-SPACE, Field of View: 224 × 224 mm, TR = 3200 ms, TE = 565 ms, Flip Angle= variable, Voxel size=0.7 mm isotropic.
Functional MRI: Gradient echo Echo Planar Imaging (EPI) sequence, Field of View: 208 × 180 mm (RO×PE), TR = 720 ms, TE = 33.1 ms, Flip Angle= 52, Voxel size: 2.0 mm isotropic, 72 slices.
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Retrospective Analysis of GBM Surgical Outcomes

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This retrospective observational study involved 64 patients diagnosed with GBM who underwent surgery at our institution between 1 January 2012 and 1 September 2021. Patients’ data collection included clinical data and all MRI images on pre- and post-operative tumor localization, volume in contrast-enhanced T1 sequences, area volume of FLAIR abnormalities, and the presence of edema. MRI images were acquired through a 3 T scanner (Siemens) 48 h after surgery, and tumor volumes were analyzed via a semiautomatic region of interest (ROI) analysis with Iplan Cranial v3.0 software (Brainlab, Feldkirchen, Germany). The study included patients who had a single surgically removable neoplastic lesion GBM on pre-operative MRI while excluding those with multicentric GBM, other primary neoplastic disorders, metastases, and infectious diseases.
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9

Functional MRI Analysis of Brain Imaging Data

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Images were acquired in a Siemens 3 T scanner. T1-weighted images were obtained using a fast spoiled gradient-echo (FSPGR) sequence (TR: 11.6 ms, TE: 4.8 ms, FA: 12, matrix size: 280 × 280, 150 slices, slice thickness: 1.00 mm). An EPI-T2* sequence allowed obtaining the functional volumes, each comprising forty 3.4 mm thick slices (TR 2500 ms, TE: 27 ms, FA: 90, matrix size: 64 × 64, 40 slices, slice thickness: 3.4 mm). Head motion was tracked by means of center of mass measurements during image acquisition. None of the participants showed head movement above voxel size acquisition after a post hoc evaluation of the six head movement parameters.
Statistical Parametric Mapping (SPM12) (Welcome Department of Imaging Neuroscience, London, UK) and the Analysis of Functional Neuroimaging software were employed for the functional MRI data analysis. Functional images were despiked Analysis of Functional NeuroImages (AFNI), corrected for motion-related artifacts (SPM12), normalized to MNI standard space (SPM12), smoothed with a 8 mm full-width-at-half-maximum Gaussian kernel (SPM12) and detrended (AFNI).
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10

Multimodal Brain Imaging in Cancer Survivors

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Imaging was obtained on a 3 T scanner (Siemens, Germany). Patients underwent an MRI of the brain, which included the standard MRI protocol (using T1-, T2-, TIRM, MPRAGE, DWI) and rs-fMRI (BOLD). The standard MRI protocol was used to exclude the presence of organic brain pathology in patients following BC treatment and in the control group. Patients were asked to remain awake, keep their eyes closed, and lie still.
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