Whole-brain imaging was acquired using a Siemens 3T Magnetom Prisma system with a 64-channel head coil. In each fMRI session, a high resolution T1 weighted MPRAGE image was acquired for visualization (repetition time (TR), 1900 ms; echo time (TE), 3.02 ms; flip angle, 9°; 160 sagittal slices; 1 × 1 × 1 mm voxels). Functional volumes were acquired using a gradient-echo echo planar sequence (TR, 2000 ms; TE, 25 ms; flip angle 90°; 40 interleaved axial slices tilted approximately 30° from the AC-PC plane; 3 × 3 × 3 mm voxels). Functional data were acquired over three runs. Each run lasted 15.1 min on average (452 acquisitions). After the functional runs, a brief in-plane anatomical T1 image was collected, which was used to define a brain mask that respected the contours of the brain and the space of the functional runs (TR, 350 ms; TE 2.5 ms; flip angle 70°; 40 axial slices; 1.5 × 1.5 × 3 mm voxels). The sequence of scans was identical on both sessions. Soft padding was used to restrict head motion throughout the experiment. Stimuli were presented on a 32-inch monitor at the back of the bore of the magnet, and participants viewed the screen through a mirror attached to the head coil. Participants used a five-button fiber optic response pad to interact with the experiment (Current Designs, Philadelphia, PA).
Magnetom prisma 3t system
Manufactured by Siemens
Sourced in Germany
The MAGNETOM Prisma 3T system is a high-field magnetic resonance imaging (MRI) scanner manufactured by Siemens. It operates at a magnetic field strength of 3 Tesla, providing high-resolution imaging capabilities. The system is designed to acquire detailed anatomical and functional data for medical diagnostic and research applications.
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8 protocols using magnetom prisma 3t system
1
Whole-Brain fMRI Acquisition and Preprocessing
2
Whole-Brain fMRI Acquisition Protocol
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Whole-brain imaging was acquired using a Siemens 3T Magnetom Prisma system with a 64-channel head coil. In each fMRI session, a high resolution T1 weighted MPRAGE image was acquired for visualization (repetition time (TR), 1900 ms; echo time (TE), 3.02 ms; flip angle, 9°; 160 sagittal slices; 1 x 1 x 1 mm voxels). Functional volumes were acquired using a gradient-echo echo planar sequence (TR, 2000 ms; TE, 25 ms; flip angle 90°; 40 interleaved axial slices tilted approximately 30° from the AC-PC plane; 3 x 3 x 3 mm voxels).
Functional data were acquired over three runs. Each run lasted 15.1 min on average (452 acquisitions). After the functional runs, a brief in-plane anatomical T1 image was collected, which was used to define a brain mask that respected the contours of the brain and the space of the functional runs (TR, 350 ms; TE 2.5 ms; flip angle 70°; 40 axial slices; 1.5 x 1.5 x 3 mm voxels). The sequence of scans was identical on both sessions. Soft padding was used to restrict head motion throughout the experiment. Stimuli were presented on a 32-inch monitor at the back of the bore of the magnet, and participants viewed the screen through a mirror attached to the head coil. Participants used a five-button fiber optic response pad to interact with the experiment (Current Designs, Philadelphia, PA).
Functional data were acquired over three runs. Each run lasted 15.1 min on average (452 acquisitions). After the functional runs, a brief in-plane anatomical T1 image was collected, which was used to define a brain mask that respected the contours of the brain and the space of the functional runs (TR, 350 ms; TE 2.5 ms; flip angle 70°; 40 axial slices; 1.5 x 1.5 x 3 mm voxels). The sequence of scans was identical on both sessions. Soft padding was used to restrict head motion throughout the experiment. Stimuli were presented on a 32-inch monitor at the back of the bore of the magnet, and participants viewed the screen through a mirror attached to the head coil. Participants used a five-button fiber optic response pad to interact with the experiment (Current Designs, Philadelphia, PA).
3
Prostate MRI in Healthy Volunteers
4
Healthy Human Brain MRI Protocol
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An in vivo data set of a healthy human brain was acquired from a 29‐year‐old male volunteer after obtaining written informed consent. It contains five repetitions of each acquisition scheme (Q 1 , Q ^ 2 Q ^ 3 )
5
Optimized Diffusion MRI Acquisition Protocol
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We analysed data from three adult volunteers previously reported in (Lampinen et al., 2020 (link)). The study was approved by the regional ethical review board in Lund and written informed consent was obtained from all volunteers prior to scanning. Measurements were performed on a MAGNETOM Prisma 3T system (Siemens Health-care, Erlangen, Germany) using a prototype spin-echo EPI sequence that facilitates user-defined gradient waveforms for diffusion encoding (Szczepankiewicz et al., 2019a (link)). Data were collected using echo times between 63 and 130 ms, repetition time of 3.4 s, voxel size of 2.5 mm3, 40 slices, matrix-size of 88 × 88, in-plane and through plane acceleration factor of 2 × 2 (GRAPPA), partial-Fourier of 3/4, band-width = 1775 Hz/pixel, and “strong ” fat saturation. Diffusion encoding was performed with gradient waveforms optimized to maximize the encoding strength per unit time and to suppress concomitant field effects (Sjölund et al., 2015 (link); Szczepankiewicz et al., 2019b (link)). A total of 270 combinations of and B were used, according to the optimized protocol in Table S1 of the Supporting Information . Total acquisition time was 15 min.
6
High-resolution and Super-resolution MRI Acquisition
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Real data experiments were conducted for the acquisition protocols HR, SRrot4, and SRsh4 on a healthy volunteer after written informed consent in accordance with local ethics. The magnitude MS images were acquired in an interleaved fashion using a T2-weighted 2D FSE sequence on a Siemens Magnetom Prisma 3T system. TR/TE was set to 12,150/97 ms. The resolution was 1 × 1 × 1 mm3 for the HR protocol and 1 × 1 × 4 mm3 for the SRrot4 and SRsh4 protocols. The FOV was 256 × 256 × 192 mm3 for the SR protocols, while it was reduced to 256 × 256 × 128 mm3 for the HR protocol, since 128 was the maximum number of slices for acquisition allowed by the system. The acquisition time for a single MS image tacq/N and the total acquisition time tacq for all the protocols are reported in Table 1 . The HR protocol scan time is approximately equal to 2/3 of the SR protocols scan time, as only 2/3 of the field of view of the SR protocols is covered. GRAPPA with an acceleration factor of 2 was adopted in combination with the SMF technique, which is provided as “adaptive combine” on the employed MRI scanner. Two repetitions of the experiment (test-retest) were performed for each protocol.
7
Optimized Diffusion MRI Acquisition Protocol
8
Individual Head Modeling for Neuromodulation
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Individual magnetic resonance images obtained with a Siemens Magnetom Prisma 3T system (Siemens, Erlangen, Germany) were used to create an individual head model for each subject. The subjects were scanned using a T1 Sag MPR 1 mm ISO sequence (repetition time TR of 2,300 ms; echo time TE of 1.69 ms; field of view 288 mm; slice slab 256 mm; voxel size of 1 × 1 × 1 mm and total acquisition time 5 min 12 s).
Subsequently, to obtain accurate positions for the individual electrodes on the scalp, the head of the subject was targeted by a sensor-registration system determining the 3-dimensional position of each of 256 sensors (neuromodulation electrodes). Electrode sensor positions of the 256-channel HydroCel Geodesic Sensor Net (HCGSN) 100 (EGI, Eugene, OR, United States) were digitalized with a GPS (EGI, Eugene, OR, United States) (Luu et al., 2016 (link)).
Subsequently, to obtain accurate positions for the individual electrodes on the scalp, the head of the subject was targeted by a sensor-registration system determining the 3-dimensional position of each of 256 sensors (neuromodulation electrodes). Electrode sensor positions of the 256-channel HydroCel Geodesic Sensor Net (HCGSN) 100 (EGI, Eugene, OR, United States) were digitalized with a GPS (EGI, Eugene, OR, United States) (Luu et al., 2016 (link)).
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