Magnetic resonance images (MRI) of the foot were acquired using a Siemens Magnetom Trio 3T MRI scanner (Siemens Medical Systems, Malvern, PA) with previously published acquisition parameters.5 The foot images were obtained in supine position with the foot placed inside a head coil. Coronal images were acquired from the posterior calcaneus to the toes. Transverse images were oriented in a plane perpendicular to the posterior tibialis tendon, just distal of the talocrural joint and progressing proximal. Sagittal images included the entire foot.
3t magnetom trio mri scanner
Manufactured by Siemens
Sourced in Germany
The 3T Magnetom Trio MRI scanner is a magnetic resonance imaging system designed and manufactured by Siemens. It operates at a field strength of 3 Tesla, providing high-quality imaging capabilities. The core function of the Magnetom Trio is to generate detailed, high-resolution images of the human body for medical diagnostic purposes.
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12 protocols using 3t magnetom trio mri scanner
1
3T MRI Acquisition of the Foot
2
Multimodal Neuroimaging of Brain Activity
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Brain activity was recorded with 248 magnetometers in blocks of 30 trials at a sampling rate of 1017.25 Hz using the Magnes 3600 WH MEG system from 4D-Neuroimaging (San Diego, United States of America). This resulted in a total of three ∼13-min MEG recording runs per participant. At the beginning and at the end of each recording run, the participant’s head position was determined. Cardiac and ocular activity were recorded at a sampling rate of 5,000 Hz using electrocardiography (ECG) and electrooculography (EOG) with the BrainAmp ExG MR system from Brain Products (Gilching, Germany). Eye movements were recorded at a sampling rate of 1,000 Hz using the EyeLink 1000 Long Range eye tracker from SR Research (Ottawa, Ontario, Canada).
At the beginning of each recording run and after every six trials, the eye tracker was calibrated using EyeLink’s 13-point calibration method (SR Research Ltd., 2009 ). If the average deviation was above 0.5° or the maximum deviation at one of the calibration points was higher than 2°, the calibration was repeated.
A structural MR scan was performed with a MAGNETOM Trio 3T MRI scanner from Siemens (Munich, Germany) using MPRAGE (Mugler and Brookeman, 1990 (link)). The MR scan was used for the localization of the sources in the brain that gave rise to the signal recorded at the MEG sensors.
At the beginning of each recording run and after every six trials, the eye tracker was calibrated using EyeLink’s 13-point calibration method (SR Research Ltd., 2009 ). If the average deviation was above 0.5° or the maximum deviation at one of the calibration points was higher than 2°, the calibration was repeated.
A structural MR scan was performed with a MAGNETOM Trio 3T MRI scanner from Siemens (Munich, Germany) using MPRAGE (Mugler and Brookeman, 1990 (link)). The MR scan was used for the localization of the sources in the brain that gave rise to the signal recorded at the MEG sensors.
3
Retinotopic Mapping of Visual Cortex Using fMRI
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The main details of the experiment being compared to were discussed in Puckett et al. ( 2016), but are briefly outlined here. Six subjects had MRI scanning performed upon them with a Siemens MAGNETOM Trio 3 T MRI scanner. Several T1-weighted anatomical images were collected and then aligned through a rigid body transformation to allow for estimation of distances along the cortex. The functional data were obtained using a gradient-echo sequence with a matrix size of 240×240 and an FOV of 192 mm, resulting in an in-plane resolution of 0.8 mm × 0.8 mm.
Visual stimulation was done on a white screen viewed via a mirror. The stimulus itself was a ring stimulus with a checkerboard pattern at an eccentricity of 2 degrees, flickering every 250 ms. This was presented for 4 s, before being removed for 16.5 s. This cycle was repeated 8 times per run, giving a 3 min run, and 18-25 runs were collected per subject. Retinotopic maps were also obtained to ensure accurate mapping of the activity onto the cortex; this was done using a rotating bowtie stimulus, as in Schira et al. (2009) , for 2 runs of 6 min each.
Visual stimulation was done on a white screen viewed via a mirror. The stimulus itself was a ring stimulus with a checkerboard pattern at an eccentricity of 2 degrees, flickering every 250 ms. This was presented for 4 s, before being removed for 16.5 s. This cycle was repeated 8 times per run, giving a 3 min run, and 18-25 runs were collected per subject. Retinotopic maps were also obtained to ensure accurate mapping of the activity onto the cortex; this was done using a rotating bowtie stimulus, as in Schira et al. (2009) , for 2 runs of 6 min each.
4
Multimodal MRI Acquisition Protocol
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MR examination was performed on a Siemens 3 T Magnetom Trio MRI scanner (Siemens, Erlangen, Germany) with a 12 channel matrix head coil. Before the first test session, the scanning equipment was introduced by means of a dummy scanner to ensure the participants' comfort with the scanning environment.
A DTI SE-EPI (diffusion weighted single shot spin-echo echoplanar imaging) sequence ([TR] = 8000 ms, [TE] = 91 ms, voxel size = 2.2 × 2.2 × 2.2 mm3, slice thickness = 2.2 mm, [FOV] = 212 × 212 mm2, 60 contiguous sagittal slices covering the entire brain and brainstem) was acquired. A diffusion gradient was applied along 64 noncollinear directions with a b-value of 1000 s/mm2. Additionally, one set of images with no diffusion weighting (b = 0 s/mm2) was acquired.
Moreover, a high resolution T1-weighted image was acquired for anatomical detail using a 3D magnetization prepared rapid acquisition gradient echo (MPRAGE; repetition time [TR] = 2300 ms, echo time [TE] = 2.98 ms, voxel size = 1 × 1 × 1.1 mm3, slice thickness = 1.1 mm, field of view [FOV] = 256 × 240 mm2, 160 contiguous sagittal slices). These structural MRI scans were examined by an expert neuro-radiologist as described previously (seeSubsection 2.1 ). The scan time for the T1 and diffusion MRI scans was approximately 25 min.
A DTI SE-EPI (diffusion weighted single shot spin-echo echoplanar imaging) sequence ([TR] = 8000 ms, [TE] = 91 ms, voxel size = 2.2 × 2.2 × 2.2 mm3, slice thickness = 2.2 mm, [FOV] = 212 × 212 mm2, 60 contiguous sagittal slices covering the entire brain and brainstem) was acquired. A diffusion gradient was applied along 64 noncollinear directions with a b-value of 1000 s/mm2. Additionally, one set of images with no diffusion weighting (b = 0 s/mm2) was acquired.
Moreover, a high resolution T1-weighted image was acquired for anatomical detail using a 3D magnetization prepared rapid acquisition gradient echo (MPRAGE; repetition time [TR] = 2300 ms, echo time [TE] = 2.98 ms, voxel size = 1 × 1 × 1.1 mm3, slice thickness = 1.1 mm, field of view [FOV] = 256 × 240 mm2, 160 contiguous sagittal slices). These structural MRI scans were examined by an expert neuro-radiologist as described previously (see
5
Multimodal Brain Imaging Protocol
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From all participants, three types of MRI scans were obtained using a Siemens 3T Magnetom Trio MRI scanner with a 32-channel head coil. First, T1-MPRAGE anatomic images were acquired (160 slices, TR = 1750 ms, TE = 4.18 ms, field of view = 256 mm, flip angle = 9°, voxel size = 1 × 1 × 1 mm, TA = 4:05 min). Next, resting-state functional echo-planar imaging (EPI) data were obtained in an interleaved order (42 slices, TR = 2100 ms, TE = 27 ms, field of view = 192 mm, flip angle = 90°, voxel size = 3 × 3 × 3 mm, TA = 6:24 min). After the first 4 control subjects, 5 meningioma patients, and 2 glioma patients were scanned, the fMRI protocol was accidentally changed to a TR of 2400 ms, resulting in a TA of 7:19 min. This has been taken care of in subsequent analyses by inclusion of an additional covariate. During the fMRI scan, participants were instructed to keep their eyes closed and not fall asleep. Finally, a multishell high-angular resolution diffusion-weighted MRI (DWI) scan was acquired (60 slices; TR = 8700 ms; TE = 110 ms; field of view = 240 mm; 101 diffusion directions; b-values = 0, 700, 1200, 2800 s/mm2; voxel size = 2.5 × 2.5 × 2.5 mm; TA = 15:14 min). In addition, two DWI b = 0 s/mm2 images were collected with reversed phase-encoding blips for the purpose of correcting susceptibility-induced distortions (Andersson et al., 2003 (link)).
6
Multimodal MRI Acquisition and Preprocessing Protocol
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A Siemens 3T Magnetom Trio MRI scanner with a 12-channel head coil was used to obtain T1 and rs-fMRI image data. T1 images were acquired with the parameters of repetition time (TR)=1,670 ms, echo time (TE)=1.89 ms, field of view=250 mm, flip angle=9°, voxel size=1.0×1.0×1.0 mm3, and 208 sagittal slices. Rs-fMRI images were obtained with the parameters of TR=3,500 ms, TE=30 ms, FOV=240 mm, flip angle=90°, voxel size=1.9×1.9×3.5 mm3, 35 slices, and 116 volumes. Participants were told to close their eyes and be as still as possible during the image acquisition, which lasted for 6 minutes and 58 seconds.
We excluded subjects with head motion exceeding the criteria (translation >2.0 mm and rotation >2.0°), and data were preprocessed using CONN toolbox version 19c (www.nitrc. org/projects/conn) implemented in MATLAB version 2020a [26 (link)]. The images were realigned and unwarped for motion estimation and were processed by slice-timing correction. Then, outliers were detected through ART-based scrubbing. Then, the images were coregistered using structural and functional images, segmented on structural images and normalized to Montreal Neurology Institute (MNI) space. Finally, the images were smoothed with a 6 mm full-width at half-maximum (FWHM) Gaussian kernel.
We excluded subjects with head motion exceeding the criteria (translation >2.0 mm and rotation >2.0°), and data were preprocessed using CONN toolbox version 19c (www.nitrc. org/projects/conn) implemented in MATLAB version 2020a [26 (link)]. The images were realigned and unwarped for motion estimation and were processed by slice-timing correction. Then, outliers were detected through ART-based scrubbing. Then, the images were coregistered using structural and functional images, segmented on structural images and normalized to Montreal Neurology Institute (MNI) space. Finally, the images were smoothed with a 6 mm full-width at half-maximum (FWHM) Gaussian kernel.
7
Resting-State fMRI Acquisition Protocol
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Magnetic resonance imaging (MRI) scans were performed on a Siemens 3-T Magnetom Trio MRI scanner (Siemens AG, Erlangen, Germany) with a 32-channel head coil. The MRI protocol took approximately 20 min and comprised a T1-weighted anatomical MPRAGE sequence (TR = 2,530 ms, TE = 4.94 ms, TI = 1,100 ms, flip angle = 7°, voxel size = 1 mm × 1 mm × 1 mm, 176 slices) and an rsfMRI sequence (TR = 2,000 ms, TE = 30 ms, flip angle = 78°, voxel size = 3 mm × 3 mm × 3 mm, 238 volumes). For the rsfMRI sequence, subjects were instructed to close their eyes and let their thoughts flow freely.
8
Functional MRI of Behavioral Task
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While performing the behavioral task described above, subjects underwent functional MRI scanning in a Siemens 3T Magnetom Trio MRI Scanner with a 32-channel, radiofrequency head coil. Both structural (T1-weighted MPRAGE sequence, 176 high-resolution slices, TR = 1550ms, TE = 2.39, voxel size = 0.9 mm X 0.9 mm X 0.9 mm, FOV = 220 mm, flip angle = 9°), and functional (T2-weighted EPI sequence, 33 slices, TR = 2,000 ms, TE = 30 ms, voxel size = 3 mm X 3 mm X 3 mm, FOV = 192 mm, flip angle = 80°). Approximately 1,400 volumes per subject were collected over 50 minutes while subjects performed the task.
9
Functional MRI Analysis of Decision-Making Processes
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Structural and functional images were acquired at Ghent University Hospital using a Siemens 3T Magnetom Trio MRI scanner.
Preprocessing and Generalized Linear Model. EPI images were 1) aligned to the first image in each time session, 2) corrected for slice acquisition timing; then the mean functional image was co-registered to the individual anatomical volume. The co-registered images were not normalized or smoothed.
A general linear model was then applied to the resulting voxel-level time-series in each block. The regressors of this analysis were generated through convolving the time-series impulse function for each of the 24 task states (6 decisions across 4 sequences) as well as motion parameters and global signal, with a canonical hemodynamic response function.
Preprocessing and Generalized Linear Model. EPI images were 1) aligned to the first image in each time session, 2) corrected for slice acquisition timing; then the mean functional image was co-registered to the individual anatomical volume. The co-registered images were not normalized or smoothed.
A general linear model was then applied to the resulting voxel-level time-series in each block. The regressors of this analysis were generated through convolving the time-series impulse function for each of the 24 task states (6 decisions across 4 sequences) as well as motion parameters and global signal, with a canonical hemodynamic response function.
10
Functional MRI Analysis of Decision-Making Processes
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Structural and functional images were acquired at Ghent University Hospital using a Siemens 3T Magnetom Trio MRI scanner.
Preprocessing and Generalized Linear Model. EPI images were 1) aligned to the first image in each time session, 2) corrected for slice acquisition timing; then the mean functional image was co-registered to the individual anatomical volume. The co-registered images were not normalized or smoothed.
A general linear model was then applied to the resulting voxel-level time-series in each block. The regressors of this analysis were generated through convolving the time-series impulse function for each of the 24 task states (6 decisions across 4 sequences) as well as motion parameters and global signal, with a canonical hemodynamic response function.
Preprocessing and Generalized Linear Model. EPI images were 1) aligned to the first image in each time session, 2) corrected for slice acquisition timing; then the mean functional image was co-registered to the individual anatomical volume. The co-registered images were not normalized or smoothed.
A general linear model was then applied to the resulting voxel-level time-series in each block. The regressors of this analysis were generated through convolving the time-series impulse function for each of the 24 task states (6 decisions across 4 sequences) as well as motion parameters and global signal, with a canonical hemodynamic response function.
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