The study was conducted at Dar-Alateeba Hospital, a private hospital located in Khartoum State, Sudan. The measurements involved the use of a 1.5 T whole-body Philips-MRI scanner. The scanner was equipped with high performance gradients with a maximum strength of 40 mT/m and a maximum slew rate of 200 T/m/s. A four-element torso phased array coil was used for all the scans. The research work explored the best settings that can be used in patients’ measurement via investigations conducted first on a phantom, on healthy volunteers and finally on patients as described in the following subsections.
Mri scanner
Manufactured by Philips
Sourced in Netherlands, Germany
The Philips MRI scanner is a medical imaging device that uses strong magnetic fields and radio waves to create detailed images of the inside of the human body. It is designed to capture high-quality images of organs, tissues, and other structures without the use of ionizing radiation.
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Lab products found in correlation
32 channel head coil, by Philips (6 mentions)
8 channel head coil, by Philips (3 mentions)
Standard quadrature head coil, by Philips (3 mentions)
Quadrature head coil, by Philips (3 mentions)
8 channel sense head coil, by Philips (2 mentions)
Achieva scanner, by Philips (2 mentions)
Intera scanner, by Philips (2 mentions)
Sense phased array head coil, by Philips (1 mentions)
Magnetom allegra, by Siemens (1 mentions)
Tim trio scanner, by Siemens (1 mentions)
32 channel phased array head coil, by Philips (1 mentions)
77 protocols using mri scanner
1
Optimizing MRI Protocols for Patients
2
Multimodal Brain Imaging with 3T MRI
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The patient underwent MRI by using a 3 T Philips MRI scanner (Phillips Health care, Best, The Netherlands) with a 32-channel head coil. Data were acquired in the form of single-shot spin-echo echo-planar images, with axial slices covering the whole brain across 75 interleaved slices of 2.0 mm thickness [no gap; repetition time/echo time = 1000/75 ms; field of view = 230.4 × 230.4 mm2; matrix = 144 × 144; voxel size = 2 × 2 × 2 mm3 (isotropic), number of excitations = 1]. Diffusion-sensitizing gradients were applied in 32 noncollinear directions with a b-value of 1,000 ms/mm2. The b = 0 images were scanned before acquisition of the diffusion-weighted images, with 33 volumes acquired in total.
3
Investigating Neural Correlates of Dance Movement Perception
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During identical pre- and posttraining fMRI sessions, participants completed two runs containing 80 trials each (64 stimuli, 6 attentional test videos, and 10 still-body sequences). All stimuli were novel to participants during the pretraining fMRI scan. Each video was followed by one of two questions that required participants to aesthetically rate the observed dance movement (“How much did you like the movement you just watched?”) or assess their physical ability to reproduce the movement (“How well could you reproduce the movement you just watched?”; see Fig.1 B).
The experiment was carried out in a 3T Philips MRI scanner using a SENSE phased-array head coil. For functional imaging, a single-shot echo planar imaging sequence was used (T2*-weighted, gradient echo sequence; echo time TE = 30 ms; flip angle, 90°). The scanning parameters were as follows: repetition time TR = 2000 ms; 30 axial slices; voxel dimensions, 3 mm3 with voxel slice thickness of 4 mm and slice gap of 0.8 mm; field of view (FOV), 230 × 230 × 143 mm3; matrix size, 128 mm2; anterior–posterior phase encoding. Parameters for T1-weighted anatomical scans were 240 mm2 matrix; voxel dimensions = 2 mm3; TR = 12 ms; TE = 3.5 ms; and flip angle = 8°. For each run of each scanning session, the first two brain volumes were discarded to reduce saturation effects.
The experiment was carried out in a 3T Philips MRI scanner using a SENSE phased-array head coil. For functional imaging, a single-shot echo planar imaging sequence was used (T2*-weighted, gradient echo sequence; echo time TE = 30 ms; flip angle, 90°). The scanning parameters were as follows: repetition time TR = 2000 ms; 30 axial slices; voxel dimensions, 3 mm3 with voxel slice thickness of 4 mm and slice gap of 0.8 mm; field of view (FOV), 230 × 230 × 143 mm3; matrix size, 128 mm2; anterior–posterior phase encoding. Parameters for T1-weighted anatomical scans were 240 mm2 matrix; voxel dimensions = 2 mm3; TR = 12 ms; TE = 3.5 ms; and flip angle = 8°. For each run of each scanning session, the first two brain volumes were discarded to reduce saturation effects.
4
Resting-state fMRI Acquisition Protocol
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All subjects were scanned on a 3.0-Tesla Philips MRI scanner. Resting-state functional images were obtained by using an echo-planar imaging sequence (EPI：a fast magnetic resonance imaging technique that allows acquisition of single images in as little as 20 msec and performance of multiple-image studies in as little as 20 seconds；for more information see [25 (link)]) with the following parameters: 140 time points; repetition time (TR) = 3000 ms; echo time (TE) = 30 ms; flip angle = 80°, number of slices = 48; slice thickness = 3.3 mm spatial resolution = 3×3×3 mm3 and matrix = 64×64. All original image files are available to the general scientific community.
5
Whole-Brain MRI for AD and bvFTD
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All participants underwent whole-brain T1-weighted imaging using a 3T Philips MRI scanner with standard quadrature head coil (eight channels) using the following sequences: coronal orientation, matrix 256 × 256, 200 slices, 1 mm2 in-plane resolution, slice thickness 1 mm, echo time/repetition time = 2.6/5.8 ms, flip angle α = 19°. A structural scan was not available for one control participant. All scans were examined by a neuroradiologist for structural abnormalities; none were reported for control participants. AD patients displayed characteristic MTL atrophy involving the hippocampus bilaterally, in the context of frontal and parietal atrophy. BvFTD patients displayed significant prefrontal and anteromedial temporal lobe atrophy including the hippocampus bilaterally.
6
Aging and Dementia Effects on Brain Connectivity
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This study, which was conducted at Northeastern University in 2018, contained a total of 97 participants (aged 61–85 years; average 74 years; 54 males) divided into two groups: NC and AD. All participants were recruited from public resting-state fMRI datasets of the Alzheimer’s disease Neuroimaging Initiative (http://adni.loni.ucla.edu ). AD patients had a Mini-Mental State Examination score of 17–26 (Tombaugh and McIntyre, 1992) and a Clinical Dementia Rating (Morris, 1993) of 0.5 or 1.0. Participants in the NC group were non-demented, non-depressed, and had an Mini-Mental State Examination score of 24–30 and Clinical Dementia Rating of 0. Demographic and clinical characteristics of the two groups are shown in Table 1
All participants underwent a scan session for brain imaging on a Philips MRI scanner with a 3.0-Tesla field strength. An echo-planar imaging sequence was used to collect resting fMRI scans with the following parameters: flip angle = 80.0°; axial slices = 48; slice thickness = 3.313 mm; slice acquisition order = sequential ascending; echo time = 30 ms; and repetition time = 3000 ms.
All participants underwent a scan session for brain imaging on a Philips MRI scanner with a 3.0-Tesla field strength. An echo-planar imaging sequence was used to collect resting fMRI scans with the following parameters: flip angle = 80.0°; axial slices = 48; slice thickness = 3.313 mm; slice acquisition order = sequential ascending; echo time = 30 ms; and repetition time = 3000 ms.
7
Resting-State fMRI Preprocessing Pipeline
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The details about brain imaging data acquisition and preprocessing can be found in one of our recently published studies (14 (link)). Briefly, rs-fMRI and T1-weighted structural images were scanned for each participant on a 3.0 T Philips MRI scanner (repetition time = 2,000 ms, echo time = 30 ms, slice number = 36, field of view = 240 × 240 mm2, acquisition matrix = 144 × 144, flip angle = 90°, and number of time points = 250 for rs-fMRI images; repetition time = 7.5 ms, echo time = 3.7 ms, slice number = 180, field of view = 240 × 240 mm2, acquisition matrix = 256 × 200, and flip angle = 8° for T1-weighted images). Data preprocessing was performed using the standard pipeline of the DPARSF software (32 (link), 33 (link)), including discarding the first 10 volumes, slice timing, head motion realignment, brain segmentation, spatial normalization, temporal filtering (0.01–0.10 Hz), and regressing out nuisance factors including the Friston-24 head motion parameters (34 (link)) as well as white matter and cerebrospinal fluid signals. Global signal regression (GSR) was not performed as it is still a controversial preprocessing option in rs-fMRI studies (35 (link)). Subjects with excessive head motion were excluded from the analysis, as determined by a mean framewise-displacement (FD) (36 (link)) > 0.2 mm.
8
Multimodal MRI data collection protocol
9
Multimodal MRI Protocol for Brain Imaging
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All participants underwent whole-brain T1- and diffusion- weighted images using a 3T Philips MRI scanner with standard quadrature head coil (8 channels).
The 3D T1-weighted images were acquired using the following sequences: coronal orientation, matrix 256×256, 200 slices, 1×1 mm2 in-plane resolution, slice thickness 1 mm, echo time/repetition time = 2.6/5.8 ms, flip angle α = 19°.
The diffusion-weighted sequences were acquired as follows: 32 gradient direction diffusion-weighted sequence (repetition time/echo time/inversion time: 8400/68/90 ms; b-value = 100 s/mm2; 55 2.5 mm horizontal slices, end resolution: 2.5×2.5×2.5 mm3; field of view 240×240 mm, 96×96 matrix; repeated twice). Two diffusion tensor imaging sequences were acquired for each participant, which were subsequently averaged. All scans were then visually inspected for field inhomogeneity distortions and corrected for eddy current distortions. Diffusion tensor models were fitted at each voxel via FMRIB's software library (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT ) which resulted in the creation of maps of three eigenvalues (λ1, λ2, λ3) allowing the calculation of fractional anisotropy for each participant.
The 3D T1-weighted images were acquired using the following sequences: coronal orientation, matrix 256×256, 200 slices, 1×1 mm2 in-plane resolution, slice thickness 1 mm, echo time/repetition time = 2.6/5.8 ms, flip angle α = 19°.
The diffusion-weighted sequences were acquired as follows: 32 gradient direction diffusion-weighted sequence (repetition time/echo time/inversion time: 8400/68/90 ms; b-value = 100 s/mm2; 55 2.5 mm horizontal slices, end resolution: 2.5×2.5×2.5 mm3; field of view 240×240 mm, 96×96 matrix; repeated twice). Two diffusion tensor imaging sequences were acquired for each participant, which were subsequently averaged. All scans were then visually inspected for field inhomogeneity distortions and corrected for eddy current distortions. Diffusion tensor models were fitted at each voxel via FMRIB's software library (
10
Longitudinal Brain Imaging Protocol Across Cohorts
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All patient and controls from the FRONTIER database underwent the same imaging protocol with whole-brain T1-weighted images using a 3T Philips MRI scanner with standard quadrature head coil (8 channels). The 3D T1-weighted sequences were acquired as follows: coronal orientation, 1×1 mm2 in-plane resolution, slice thickness 1 mm, TR/TE = 5.8/2.6 ms. Structural T1-weighted MRI data from the Freiburg participants were acquired on a 3T Siemens TIM-Trio scanner equipped with a 12-channel headcoil using a 3D-MPRAGE sequence in sagittal orientation with 1×1 mm2 in-plane resolution, slice thickness 1 mm, and TR/TE = 2200/2.15 ms. The scanning protocols of the two sites were held constant across subjects and over time. All patients were scanned annually after a baseline scan. Controls had a baseline scan as well as a follow-up scan after two years. Median number of scans per subject was 2 (Mean = 2.6, S.D. = 0.7, range 2 to 4 scans), the mean delay between the first and last scan was 23.3 months (S.D. = 7.7, range 12 to 36.7 months).
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