3t tim trio scanner

Manufactured by Siemens

Sourced in Germany, United Kingdom, United States

The 3T Tim Trio scanner is a magnetic resonance imaging (MRI) system manufactured by Siemens. It operates at a field strength of 3 Tesla and is designed to provide high-quality imaging for a variety of medical applications.

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272 protocols using 3t tim trio scanner

Functional Brain Imaging of Autism and Depression

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Participants with ASC (n = 33) and 18 controls were scanned using a Siemens 3T Tim Trio scanner (Siemens Healthcare, Erlangen, Germany) located at the Medical Research Council Cognition and Brain Sciences Unit, Cambridge, UK. BOLD sensitive functional images were acquired with a gradient echo planar imaging sequence with the following parameters: repetition time = 2000ms, echo time = 30ms, voxel size = 3x3x3mm³, field of view = 192 x 192 mm², 64 x 64 acquisition matrix and a 78° flip angle. In all, 32 slices were acquired descending in the transverse plane (slice thickness = 3 mm, slice gap = 25%) and 260 three-dimensional volumes acquired.
Participants with a diagnosis of MDD (n = 35) and 17 controls were scanned with an identical Siemens 3T Tim Trio scanner located at the Wolfson Brain Imaging Centre, University of Cambridge, UK using the same gradient echo planar imaging sequence as described above.
Imaging data were acquired from all participants whilst in wakeful rest (i.e. without any applied stimulus) with eyes closed.

Simas T., Chattopadhyay S., Hagan C., Kundu P., Patel A., Holt R., Floris D., Graham J., Ooi C., Tait R., Spencer M., Baron-Cohen S., Sahakian B., Bullmore E., Goodyer I, & Suckling J. (2015). Semi-Metric Topology of the Human Connectome: Sensitivity and Specificity to Autism and Major Depressive Disorder. PLoS ONE, 10(8), e0136388.

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Whole-Head Magnetoencephalography Recording

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Continuous MEG data were recorded using a whole-head 306 channel (102 magnetometers, 204 planar gradiometers) Vector-view system (Elekta Neuromag, Helsinki, Finland) located at the MRC Cognition and Brain Sciences Unit, Cambridge, UK. Participants were in a seated position. Eye movements and blinks were monitored with electrooculogram (EOG) electrodes placed around the eyes, and 5 head-position indicator (HPI) coils were used to record the head position (every 200 ms) within the MEG helmet. The participants’ head shape was digitally recorded using a 3D digitizer (Fastrak Polhemus, Inc., Colchester, VA, USA), along with the positions of the EOG electrodes, HPI coils, and fiducial points (nasion, left and right periaricular). MEG signals were recorded at a sampling rate of 1000 Hz, with a band-pass filter from 0.03 to 125 Hz. To facilitate source reconstruction, 1-mm³T₁-weighted MPRAGE scans were acquired during a separate session with a Siemens 3 T Tim Trio scanner (Siemens Medical Solutions, Camberley, UK) located at the MRC Cognition and Brain Sciences Unit, Cambridge, UK.

Clarke A., Devereux B.J., Randall B, & Tyler L.K. (2014). Predicting the Time Course of Individual Objects with MEG. Cerebral Cortex (New York, NY), 25(10), 3602-3612.

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Tractography-Guided Deep Brain Stimulation

Cited 3 times

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Procedures for tractography guided surgical targeting and post-operative verification follow Riva-Posse et al. (2018) (link). An Activa PC + S™ pulse generator (Medtronic, Minneapolis, MNI) drove bilateral DBS leads (model 3387), each with 4 contacts (1.5 mm inter-contact spacing), which were implanted in the SCC region (Figure 1A) using a prospective connectomic approach and StimVision software (Noecker et al., 2017 (link)). This approach uses patient-specific deterministic tractography and anatomical images to optimize placement of the contact at the confluence point of four white matter fibers (Riva-Posse et al., 2014 (link)). In brief, magnetic resonance imaging data, (high-resolution T1 structural and diffusion-weighted) are acquired for each individual on a Siemens 3T Tim-Trio scanner (Siemens Medical Solution, Malvern, PA). Following surgery, high-resolution computed tomography (LightSpeed16, GE Medical System) images are used to verify that the contacts used for therapeutic stimulation respect to tractography.

Smith E.E., Choi K.S., Veerakumar A., Obatusin M., Howell B., Smith A.H., Tiruvadi V., Crowell A.L., Riva-Posse P., Alagapan S., Rozell C.J., Mayberg H.S, & Waters A.C. (2022). Time-frequency signatures evoked by single-pulse deep brain stimulation to the subcallosal cingulate. Frontiers in Human Neuroscience, 16, 939258.

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Magnetoencephalography Data Acquisition Protocol

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Continuous MEG data were recorded using a whole-head 306 channel (102 magnetometers, 204 planar gradiometers) Vectorview system (Elekta Neuromag) located at the MRC Cognition and Brain Sciences Unit, Cambridge, UK. Eye movements and blinks were monitored with EOG electrodes placed around the eyes, and five head position indicator coils were used to record the head position (every 200 msec) within the MEG helmet. The participants' head shape was digitally recorded using a 3-D digitizer (Fastrak Polhemus, Inc.), along with the positions of the EOG electrodes, head position indicator coils, and fiducial points. MEG signals were recorded at a sampling rate of 1000 Hz, with a band-pass filter from 0.03 to 125 Hz. To facilitate source reconstruction, 1 mm 3 T1-weighted MPRAGE scans were acquired during a separate session with a Siemens 3T Tim Trio scanner (Siemens Medical Solutions) located at the MRC Cognition and Brain Sciences Unit, Cambridge, UK.

Clarke A., Devereux B.J, & Tyler L.K. (2018). Oscillatory Dynamics of Perceptual to Conceptual Transformations in the Ventral Visual Pathway. Journal of cognitive neuroscience, 30(11).

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3T MRI Structural Brain Imaging Preprocessing

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High resolution T₁-weighted images were acquired on a Siemens 3T TIM Trio scanner with a five-echo multi-echo MPRAGE (MEMPR) sequence [TE = 1.64, 3.5, 5.36, 7.22, 9.08 ms, TR = 2.53 s, inversion time = 1.2 s, 7° flip angle, number of excitations (NEX) = 1, slice thickness = 1 mm, FOV = 256 mm, resolution = 256 × 256].
We utilized the optimized VBM pre-processing procedure and SPM12 for image pre-processing and statistical analysis (Good et al., 2001 (link)). Images were normalized to MNI space with DARTEL and segmented in SPM12, a high-dimensional normalization pipeline. The non-brain tissues were stripped and gray matter, white matter, and cerebral spinal fluid (CSF) were segmented and normalized. We completed the preprocessing pipeline in two parallel steps to create both the gray matter concentration and gray matter volume images. Following segmentation, gray matter volume images were then smoothed to an 8 mm × 8 mm × 8 mm Gaussian kernel. Both VBM and SBM analyses were performed with the gray matter concentration and volume images.

Rootes-Murdy K., Zendehrouh E., Calhoun V.D, & Turner J.A. (2021). Spatially Covarying Patterns of Gray Matter Volume and Concentration Highlight Distinct Regions in Schizophrenia. Frontiers in Neuroscience, 15, 708387.

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Multimodal MRI Protocol for Brain Imaging

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All MRI experiments were performed on a Siemens 3T TIM Trio scanner. For the Tl-weighted acquisition, Magnetization-Prepared Rapid Acquisition Gradient Echo (MPRAGE) images were acquired using a 3D inversion recovery sequence with TR/TE/TI = 2170/4.33/1100 ms. The resolution is 1×1×1mm³ with a matrix size of 256×256×192. The flip angle = 7° and total scan time was 8 minutes and 8 seconds. For perfusion imaging, pseudo continuous arterial spin labeled (pCASL) images were acquired using gradient-echo echo-planar imaging (EPI) with TR/TE = 4000/12 ms. The resolution was 3.125×3.125×6mm (5mm thickness with a 1mm gap) over a 64×64×24 matrix. 40 label/control pairs were acquired. Generalized autocalibrating partially parallel acquisition (GRAPPA) was used with an acceleration factor of 2. Labeling duration was 1.5s and the post-labeling delay was 1.2s. Total imaging time was 5 minutes and 30 seconds. Diffusion weighted images were acquired with single-shot spin-echo EPI with TR/TE = 9500/87ms. A single b=0 volume was acquired along diffusion weighted images for 30 directions with b-value=1000. The resolution was 2×2×2mm with a matrix size of 128×128×75 voxels, with a flip angle of 90°. Total acquisition time was 11 minutes with two acquisitions.

Kandel B.M., Wang D.J., Gee J.C, & Avants B.B. (2014). Eigenanatomy: Sparse Dimensionality Reduction for Multi-Modal Medical Image Analysis. Methods (San Diego, Calif.), 0, 43-53.

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Multimodal Brain Imaging Protocol

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Images were acquired with a Siemens 3T Tim Trio scanner using a 32-channel head coil at the Wolfson Brain Imaging Centre at the University of Cambridge. For anatomical reference, a T1-weighted magnetization prepared rapid gradient echo was acquired (FOV 240 x 256 x 176 mm, 1-mm-in-plane resolution, inversion time [TI] = 900 milliseconds, TR = 2300 milliseconds; TE = 2.98 milliseconds; flip angle = 9°; voxel size = 1 x 1 x 1 mm). For the acquisition of the functional images, the following parameters were used: TR = 2.32 seconds, TE = 30 milliseconds, flip angle = 78°, matrix = 64 x 64, voxel size = 3 x 3 x 3 mm³, a 25% gap between slices (0.75 mm).

Mechelmans D.J., Strelchuk D., Doñamayor N., Banca P., Robbins T.W., Baek K, & Voon V. (2017). Reward Sensitivity and Waiting Impulsivity: Shift towards Reward Valuation away from Action Control. International Journal of Neuropsychopharmacology, 20(12), 971-978.

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Structural and Functional MRI Acquisition

Cited 2 times

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Data were acquired on a Siemens 3T Tim Trio scanner equipped with a transmit-receive body coil and a commercial 12-channel head coil array as described previously [4 (link),56 (link)]. MPRAGE parameters were: 176 sagittal slices, TR/TE/TI = 1900/2.52/900 ms, FOV = 250 mm², matrix of 246x256, 1.0 mm slice thickness, and effective resolution of 1.0 mm³. fMRI acquisition during the n-back protocol used T2*-weighted echo planar imaging. Acquisition parameters were: 47 axial slices with a 3.2 mm thickness, TR/TE = 2500/30 ms, 90° flip angle, FOV = 205 mm², 64x64 matrix for an effective resolution of 3.2 mm³ [4 (link),56 (link)].

Clarke T., Jamieson J.D., Malone P., Rayhan R.U., Washington S., VanMeter J.W, & Baraniuk J.N. (2019). Connectivity differences between Gulf War Illness (GWI) phenotypes during a test of attention. PLoS ONE, 14(12), e0226481.

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3T MRI MPRAGE Structural Imaging

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Imaging at the RUBIC was conducted using a Siemens 3T Tim Trio scanner with a 32-channel head coil. 3D T1weighted sagittal magnetization-prepared rapid acquisition gradient echo (MPRAGE) structural images were obtained with the following parameters: repetition time (TR) = 2500 ms, echo time (TE) = 3.15 ms, flip-angle = 8, Field-of-View (FoV) = 256 mm 2 , resulting in 224 slices with 0.8 x 0.8 x 0.8 mm 3 voxels (Alexander et al., 2017) (link).

Yin S., Hong S., Martino A.D., Milham M.P., Park B., Benkarim O., Bethlehem R.A., Bernhardt B.C., & Paquola C. (2020). Shared and distinct patterns of atypical cortical morphometry in children with autism and anxiety.

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3T MRI Acquisition Protocol for Structural and Functional Data

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All of the MRI data were acquired with a Siemens 3T TIM Trio scanner that was equipped with a 32-channel head coil. Structural T1 images with 160 slices were collected with 1×1×1 mm voxels, 256×256 matrix, TR = 8.13 msec, TE = 3.7 msec, flip angle = 8°, slice thickness = 1.0 mm, and no slice gap. Functional T2*-weighted images with 36 slices were collected with 3×3×3 mm voxels, 64×64 matrix (FOV = 128×128) using a single shot gradient echo-planar imaging sequence, flip angle = 90°, TR = 8.6 sec, TE = 35 msec, TA = 1647 msec, transverse acquisition, slice thickness = 3.00 mm, sequential order, no slice gap, and GRAPPA-parallel imaging with acceleration factor = 2. Prior to the onset of the functional experiment, four dummy volumes were collected and discarded.

Vaden KI J.r., Kuchinsky S.E., Ahlstrom J.B., Teubner-Rhodes S.E., Dubno J.R, & Eckert M.A. (2016). Cingulo-Opercular Function during Word Recognition in Noise for Older Adults with Hearing Loss. Experimental aging research, 42(1), 67-82.

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