Allegra head only scanner

Manufactured by Siemens

Sourced in Germany

The Allegra head-only scanner is a magnetic resonance imaging (MRI) system designed for neuroimaging research. It is a specialized MRI scanner that focuses on the head and brain, providing high-quality imaging for studies and investigations related to the central nervous system.

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Lab products found in correlation

Standard head coil, by Siemens (2 mentions) 3t tim trio, by Siemens (1 mentions) E prime version 1, by Psychology Software Tools (1 mentions)

8 protocols using allegra head only scanner

Multimodal MRI Acquisition Protocol

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Most MRI data were acquired on a 3T Siemens Allegra head only scanner (Siemens Medical System, Erlangen, Germany); comprising 81% of the 1-year-olds and 72% of the 2-year-olds in the present study. For earlier Allegra diffusion weighted imaging (DWI) data, a single shot echo-planar imaging (EPI) spin-echo sequence was used with the following parameters: Repetition Time (TR)/ Echo Time (TE) = 5200/73 ms, slice thickness = 2 mm, in-plane resolution = 2 × 2 mm², with a total of 45 slices for 6 diffusion weighted images using b-value of 1000 s/mm² and 1 baseline image (b-value = 0) per sequence, repeated five times total to improve signal-to-noise. For the remaining Allegra DWI data, 42 directions of diffusion sensitization were acquired with a b-value of 1000 s/mm² in addition to seven images with no diffusion weighting for reference. The parameters were as follows: TR/TE/Flip angle = 7680/82/90°, slice thickness = 2 mm, in-plane resolution = 2 × 2 mm², with a total of 60–72 slices. The rest of the study subjects were scanned using an upgraded Siemens model, the 3T Tim Trio (Siemens Medical System, Erlangen, Germany), following the same sequencing parameters as the 42 direction Allegra sequence detailed above.

Lee S.J., Zhang J., Neale M.C., Styner M., Zhu H, & Gilmore J.H. (2018). Quantitative tract‐based white matter heritability in 1‐ and 2‐year‐old twins. Human Brain Mapping, 40(4), 1164-1173.

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High-Resolution fMRI with Susceptibility Mitigation

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Images were acquired with a 3T Siemens Allegra head-only scanner. Functional images (TR = 2000 ms; effective TE = 30 ms; flip angle = 82, 34.3 mm slices with a 0.45 mm gap for whole-brain coverage, matrix = 80 × 64; FOV = 240 × 192 mm; acquisition voxel size = 3 × 3 × 3.45 mm) were acquired using a customized multi-echo EPI sequence developed by the NYU Center for Brain Imaging to mitigate the effects of susceptibility artifacts. Five fixation scans were acquired at the start of each run and dropped from analysis to allow for magnet equilibration. Slices were collected parallel to the AC-PC line. Finally, T1-weighted high-resolution anatomical images (MPRAGE, 1 × 1 × 1 mm) were acquired for each subject for registration and group normalization purposes.

Hackel L.M., Zaki J, & Van Bavel J.J. (2017). Social identity shapes social valuation: evidence from prosocial behavior and vicarious reward. Social Cognitive and Affective Neuroscience, 12(8), 1219-1228.

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Multimodal MRI Acquisition Protocol

Cited 1 time

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MRI data were acquired using a 3-T Siemens Allegra head-only scanner with a Siemens standard head coil. High-resolution structural images (T1-weighted images) were acquired using Magnetization-Prepared Rapid Gradient-Echo sequence (37 (link)), with TR = 2 s, TE = 4.38 ms, voxel size 0.938 × 0.938 × 1, 176 slices, and 1 mm slice thickness. T2-weighted images (echo planar imaging sequence) were acquired with TR = 2s, TE = 30 ms, FOV 220 mm × 220 mm, voxel size = 3.4 mm × 3.4 mm × 4 mm, 32 slices, and 62 ms inter-slice time.

Saleh S., Fluet G., Qiu Q., Merians A., Adamovich S.V, & Tunik E. (2017). Neural Patterns of Reorganization after Intensive Robot-Assisted Virtual Reality Therapy and Repetitive Task Practice in Patients with Chronic Stroke. Frontiers in Neurology, 8, 452.

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Structural and Functional MRI Acquisition

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A 3T Siemens Allegra head-only scanner and standard head coil were used for structural and functional data acquisition at the University Heights Center for Advanced Imaging. Anatomical images were acquired using a T1-weighted protocol (256 × 256 matrix, 176 1-mm sagittal slices). Functional images were acquired using a single-shot gradient echo EPI sequence (TR = 2000 ms, TE = 20 ms, FOV = 192 cm, flip angle = 80°, bandwidth = 2604 Hz/px, echo spacing = 0.29 ms). Thirty-five contiguous oblique-axial slices (3 × 3 × 3 mm voxels) parallel to the AC-PC line were obtained.

Sip K.E., Smith D.V., Porcelli A.J., Kar K, & Delgado M.R. (2014). Social closeness and feedback modulate susceptibility to the framing effect. Social neuroscience, 10(1), 35-45.

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Multimodal Neuroimaging of Substantia Nigra

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All scanning was done on a 3 T Siemens Allegra head-only scanner (Siemens, Erlangen, Germany). A high-resolution structural scan was acquired for anatomic reference (magnetization-prepared rapid gradient echo (MPRAGE); TR/TE/inversion time = 2,300/3.93/1,100 ms, flip angle = 12°, 256 × 256 matrix, 1 mm isotropic voxels).
fMRI data were acquired using the gradient-recalled echo-planar imaging sequence (repetition time/echo time (TR/TE) = 2,000/25 ms, flip angle = 70°, field of view = 192 mm, 6 mm slice thickness, 32 axial slices). An IFIS-SA system (MRI Devices, Corp., Waukesha, WI, USA) running E-Prime (version 1.2, Psychology Software Tools Inc., Sharpsburg, PA, USA) was used to control stimulus delivery and record responses.
We used a turbo spin echo sequence with magnetization transfer contrast to visualize the SN and aid in placement of an ¹H-MRS voxel (13 × 13 × 13 mm; Figure 2) positioned around the left SN. Following manual shimming, water-suppressed spectra were collected with the point-resolved spectroscopy sequence (TR/TE = 2,000/80 ms, 640 averages; for details see refs 16, 21).

White D.M., Kraguljac N.V., Reid M.A, & Lahti A.C. (2015). Contribution of substantia nigra glutamate to prediction error signals in schizophrenia: a combined magnetic resonance spectroscopy/functional imaging study. NPJ Schizophrenia, 1, 14001-.

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High-Resolution T1-Weighted Brain Imaging

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High resolution T1-weighted scans were acquired sagitally at the NYU Center for Brain Imaging on a 3T Siemens Allegra head-only scanner. We used an MPRAGE sequence with parameters TE=3.25ms, TR=2530ms, TI=1100ms, flip angle=7.0 degrees, matrix 256×256×128, FOV=256×256×170.24mm, voxel size=1×1×1.33mm.

Butler T., Zaborszky L., Pirraglia E., Li J., Wang X.H., Li Y., Tsui W., Talos D., Devinsky O., Kuchna I., Nowicki K., French J., Kuzniecky R., Wegiel J., Glodzik L., Rusinek H., DeLeon M.J, & Thesen T. (2014). Comparison of human septal nuclei MRI measurements using automated segmentation and a new manual protocol based on histology. NeuroImage, 97, 245-251.

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3T Functional MRI Acquisition Protocol

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All MRI data were acquired on a 3T Allegra head-only scanner (Siemens, Erlangen, Germany) using a head transmit coil (NM-011) and two surface receive coils (NOVA Medical, Wakefield, MA): (1) a four-channel phased array receive surface coil (NMSC-021) for retinotopic mapping, (2) a four-element phased parallel array (NMSC-011) for memory-guided saccade tasks. We acquired T2*-sensitive echo-planar images (repetition time (TR) 1.5s; echo time 30ms; flip angle 75°; 26 slices; 3×3×3mm voxels; 192×192mm field of view). Three T1-weighted MPRAGE scans were averaged and used for gray matter segmentation, cortical flattening, registration, and visualization for creating ROIs (see below). Functional scans were corrected for head motion and aligned across sessions, detrended and high-pass filtered with a cutoff frequency of 0.0167 Hz, and converted to percentage signal modulation.

Rahmati M., Saber G.T, & Curtis C.E. (2017). Population Dynamics of Early Visual Cortex During Working Memory. Journal of cognitive neuroscience, 30(2), 219-233.

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Neuroimaging of Aversive Learning

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Data were acquired on a 3T Siemens Allegra head-only scanner. Functional images were acquired with a single shot gradient-echo echoplanar imaging sequence (64 x 64 matrix, TR = 2000 ms, TE = 30 ms, FOV = 192 cm, flip angle = 90°). We proscribed 36 continuous oblique angle slices (3 x 3 x 3 mm voxels) using a 30-degree head tilt relative to the plane defined by the anterior commissure-posterior commissure to maximize signal in the OFC / VMPFC (Deichmann et al., 2003 (link)). Minimizing dropout in this region reduced parietal cortex coverage for a number of participants; thus findings are agnostic with respect to the contribution of parietal cortex regions to aversive learning. Anatomical images were acquired with a T1-weighted protocol (256 x 256 matrix, 176 1 mm sagittal slices).

Atlas L.Y., Doll B.B., Li J., Daw N.D, & Phelps E.A. (2016). Instructed knowledge shapes feedback-driven aversive learning in striatum and orbitofrontal cortex, but not the amygdala. eLife, 5, e15192.

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