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64 protocols using eight channel head coil

1

Functional MRI Neuroimaging of Resting-State Brain

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The brains’ images of all subjects were generated by a Siemens 3.0 T scanner
(Erlangen, Germany) with an eight-channel head coil. fMRI scans were performed
during RLS-free periods and in “off” medication state to reduce the effect of
the medication on the images. During the data acquisition process, all subjects
were asked to close their eyes and lie quietly for magnetic resonance scanning.
The three-dimensional structural images were produced with a T1-weighted
Magnetization-Prepared Rapid Gradient-Echo (MP-RAGE) sequence on the condition
of repetition time = 1900 ms, echo time = 2.27 ms, flip angle = 9°,
thickness = 1.0 mm, field of view = 256 × 256 mm2, and
matrix = 256 × 256. Resting-state functional images were collected using
anecho-planar imaging sequence with 31 axial slices, repetition time = 2000 ms,
echo time = 30 ms, flip angle = 90°, thickness = 3.5 mm, gap = 0.35 mm, field of
view = 224 × 224 mm2, and matrix = 64 × 64 and 240 time points.
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2

MRI Acquisition Protocol for Functional Neuroimaging

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MRI data were acquired using a Siemens Trio 3T MRI system with an eight-channel head coil at the Shenzhen Institutes of Advanced Technology, Chinese Academy of Science. Functional MRI data were collected with EPI sequence, slice number = 33, matrix size = 64*64, FOV = 220*220mm, TR/TE = 2000/30ms, FA = 90 º, slice thickness = 3.5 mm, and gap = 0 mm. T1-weighted high-resolution structural images were acquired using a magnetization-prepared rapid acquisition gradient echo sequence (176 slices, TR = 1900 ms, TE = 2.53 ms, FA = 9 º, voxel size = 1 × 1 × 1 mm3).
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3

Multimodal Neuroimaging Protocol for Resting-State fMRI Analysis

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All subjects underwent MRI scan on the same imaging session on 3.0 Tesla MRI system with eight-channel head coil (Siemens, Erlangen, Germany) in our hospital. All participants lay in the scanner with their eyes closed and relaxed and avoided falling asleep or thinking. In order to reduce noise, all subjects were required to wear earplugs and use foam pads to decrease head movement. Firstly, the functional scans were located using a series of localizer scans. Secondly, conventional T1-weighted imaging (echo time [TE] =2.46 ms, repetition time [TR] =250 ms, field of view [FOV] =220×220 mm, gap =1.5 mm, slices =19, slice thickness =5 mm) and T2-weighted imaging (TE =113 ms, TR =4,000 ms, FOV =220×220 mm, gap =1.5 mm, slices =19, slice thickness =5 mm) were gained. Thirdly, 240 rs-fMRI images were obtained with the following parameters: TE =30 ms; TR =2,000 ms; FOV =230×230 mm; flip angle =90°; gap =1.2 mm; thickness =4.0 mm; acquisition matrix =64×64; and 30 axial slices from contiguous echo-planar imaging scans. Finally, a total of 176 high-resolution T1-weighted images were collected by using a three-dimensional spoiled gradient-recalled echo sequence in a sagittal orientation with the following parameters: TE =2.26 ms; TR =1,900 ms; gap =0 mm; thickness =1.0 mm; FOV =250×250 mm2; acquisition matrix =256×256; flip angle =9°.
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4

MRI Structural Neuroimaging Protocol

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The MRI scan was performed using a Siemens 3.0 Tesla system (Tim Trio, Siemens Healthineers, Erlangen, Germany) with an eight‐channel head coil at West China Hospital of Sichuan University, Chengdu, China. High‐resolution T1‐weighted anatomical images were obtained using a rapid gradient‐echo planar imaging sequence with acquisition parameters of repetition time = 1.96 s, echo time = 2.26 ms, flip angle = 90°, contiguous slices = 176 with a thickness of 1 mm each, matrix = 256 × 256, and field of view = 240 mm × 240 mm.
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5

Epilepsy MRI Acquisition Protocols

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Participants from UCL were scanned between January 2004 and March 2018. For those scanned between January 2004 and March 2013 (all people with IGE, 336 people with focal epilepsy and 50 control subjects) (Supplementary material, ‘Methods’ section), MRI data were acquired on a 3 T GE Signa HDx scanner with a coronal T1-weighted 3D inversion recovery fast spoiled gradient echo (IR-FSPGR) sequence, repetition time/echo time/inversion time: 8.1/3.1/450 ms, voxel size: 0.9 × 0.9 × 1.1 mm. For those scanned between March 2013 and March 2018 (355 people with focal epilepsy and 71 healthy control subjects) (Supplementary material, ‘Methods’ section), MRI data were acquired on a 3 T GE Discovery MR750 scanner using a 3D T1-weighted magnetization prepared rapid acquisition gradient echo (MPRAGE) sequence with echo time/repetition time/inversion time: 3.1/7.4/400 ms, voxel size: 1.0 × 1.0 × 1.0 mm. For participants in the external validation cohort, MRI data were acquired at the West China Hospital between June 2013 and December 2020, using a 3 T Siemens Tim Trio MRI scanner with an eight-channel head coil. High-resolution T1-weighted MRI was acquired using a 3D MPRAGE sequence with repetition time/echo time/inversion time: 1900/2.6/900 ms, voxel size: 1.0 × 1.0 × 1.0 mm.
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6

High-resolution 3T MRI Brain Imaging

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MRI scanning was performed on a 3-T MRI scanner (Siemens, Erlangen, Germany) with an eight-channel head coil. High-resolution T1-weighted images were acquired using a three-dimensional spoiled gradient-recalled sequence with the following parameters: repetition time=1900 ms, echo time=2.26 ms, thickness=1.0 mm, gap=0.5 mm, acquisition matrix=256×256, field of view=250×250 mm, flip angle=9°, and slices=176.
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7

Resting-state fMRI and Structural MRI Acquisition

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Anatomical MRI scans and resting-state fMRI scans were acquired on a 3T Siemens scanner (MAGNETOM Trio Tim, Siemens, Germany) using an eight-channel head coil at the Shenzhen Children's Hospital, Guangdong, China. Foam cushions were used in the scanning process to reduce head translation movement and rotation. High-resolution T1-weighted 3D MPRAGE images were acquired for almost all subjects except one control subject: TR/TE = 2,300/2.26 ms, FOV = 200 × 256 mm2, 160 slices, 1 mm slice thickness, flip angle = 8°. Resting blood oxygen level-dependent data were acquired in each subject (expect one patient) using an echo-planar imaging sequence with the following scan parameters: TR/TE = 2,000/30 ms, FOV = 220 × 220 mm2, matrix = 94 × 94, flip angle = 90°, slice thickness = 3 mm, 36 interleaved axial slices, and 130 volumes. All participants were instructed to lie still with their eyes closed while remaining awake. All acquisitions were visually inspected for imaging artifacts, and none of the participants were excluded on this basis.
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8

Multimodal Neuroimaging Protocol for Resting-State and Pain Experiments

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All data was collected on a Siemens 3 Tesla MR scanner using a PET-compatible eight-channel head coil. Structural T1 weighted MPRAGE images were collected with the following parameters: voxel size 1 × 1 × 1 mm; TR = 2530 ms; TE = 1.63 ms, 3.49 ms, 5.35 ms and 7.21 ms, flip angle = 7°; rs-fMRI and pain paradigm fMRI images were with the following parameters: multi-slice T2*-weighted echo-planar images, voxel size 3.1 × 3.1 × 3.1 mm, TR = 2000 ms, TE = 30 ms, flip angle = 90°, number of slices = 37. Two sets of 184 volumes (6 min, 14 s) of resting state data were collected for each of the two PET-MR scans. Four sets of 250 volumes (8 min, 26 s) of pain experiment data, as described in Fig. 1, were collected for each of the two PET-MR scans.
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9

Neuroimaging of Participants in Yantai Hospital

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All the participants were scanned using a 3.0-T Siemens scanner with an eight-channel head coil in Yantai Affiliated Hospital of Binzhou Medical University. Foam pads and earplugs were used to reduce the head motion and scanner noise. Functional images were obtained using a gradient echo-planar imaging (EPI) sequence (TR = 2000 ms, TE = 30 ms, voxel size = 3.1 mm × 3.1 mm × 4.0 mm, matrix size = 64 × 64, slices = 33, slices thickness = 4 mm, slice gap = 0.6 mm). In addition, a three-dimensional magnetization-prepared rapid-acquisition gradient echo (3D MPRAGE) sequence (TR = 1900 ms, TE = 2.52 ms, TI = 1100 ms, voxel size = 1 mm × 1 mm × 1 mm, matrix size = 256 × 256) was used to acquire the T1-weighted anatomical images. The stimuli were displayed by high-resolution stereo 3D glasses within a VisualStim Digital MRI Compatible fMRI system (Choubey et al., 2009 (link); Liang et al., 2017 (link); Yang et al., 2018 (link)).
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10

High-Resolution MRI Acquisition and Functional Imaging

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Magnetic resonance imaging was performed using a 3.0-T scanner (Siemens Trio Tim, Erlangen, Germany) with an eight-channel head coil. During the scanning, the participants were instructed to stay relaxed, stay awake with their eyes closed and remain as motionless as possible. Earplugs and foam pads are used to reduce scanner noise and minimize head movement. First, high-resolution anatomic images using a 3D T1-weighted spoiled gradient recall (3D T1-SPGR) sequence were acquired with the following parameters: repetition time (TR) = 1900 ms, echo time (TE) = 2.26 ms, flip angle (FA) = 9°, field of view (FOV) = 250 × 250 mm, matrix = 256 × 256, 176 slices, slice thickness = 1 mm, voxel size = 1.0 × 1.0 × 1.0 mm3, and interslice gap = 0.5 mm. For the functional scans, the parameters were TR/TE = 2000/30 ms, flip angle = 90°, FOV = 200 × 200 mm, matrix = 64 × 64, voxel size = 3.0 × 3.0 × 4.0 mm3, slice thickness = 4.0 mm, gap = 1.2 mm, voxel size = 3.0 × 3.0 × 4.0 mm3, and 240 time points (8 min, 6 s).
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