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86 protocols using 3t scanner

1

Resting-state fMRI acquisition protocol

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For data acquisition, six sites used Siemens 3 T (T) scanners, two sites used Philips 3 T scanners, and one site used a GE 3 T scanner (see Supplemental Table S1 and Table S2 for detailed scanner specifications). T1-weighted anatomical scans and T2*-weighted echo-planar resting state functional imaging were performed with predominantly similar parameters across sites (TR 2.45 s or less, at least 32 slices). The average acquisition time was 8 min 25 s. The participants were instructed in a standardized fashion to lie still, look at a white crosshair presented against a black background, not think about anything specific, and let their mind wander (to avoid constraining spontaneous thoughts [35 (link)]).
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2

Multimodal MRI Neuroimaging Protocol

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Participants were scanned with General Electric Healthcare 3 T scanners at various participating sites. T1-weighted images were acquired using a 3D IR-SPGR protocol (TE = 3.036 s; TR = 7.34 s; TI = 400 ms; 256 × 256 matrix; 196 sagittal slices; in-plane resolution = 1.0156 mm; slice thickness = 1.2 mm). DTI images were acquired with an EPI SE protocol (TE = 90 ms; TR = 9.05 s; 256 × 256 matrix, 59 axial slices, in-plane resolution = 1.37 mm; slice thickness = 2.7 mm; diffusion-weighted volumes in 41 directions; b-value = 1000 s/mm2). Further information regarding these protocols is available online (http://adni.loni.usc.edu/methods/documents/mri-protocols/).
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3

MRI Acquisition and Analysis for MCSA

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MRI for MCSA participants was acquired on 3T scanners (General Electric Healthcare, Waukesha, WI, USA) using protocols aligned with ADNI.36 (link) Information for acquisition and processing has been described elsewhere.37–39 (link) Hippocampal volume and ICV were derived using FreeSurfer (version 5.3).
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4

Multi-site fMRI Harmonization Protocol

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MRI imaging was performed across all 21 sites within the United States, harmonized across Siemens Prisma, Philips, and GE 3 T scanners. Details on image acquisition can be found in Casey et al. (2018) (link). All functional data were acquired using a gradient-echo EPI sequence (TR =800 ms, TE =30 ms, flip angle = 90°, voxel size = 2.4 mm3, 60 slices).
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5

Multimodal Brain Imaging Protocol for Alzheimer's Disease

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DTI and inversion-recovery spoiled gradient recalled (IR-SPGR) T1-weighted imaging data were acquired on several General Electric 3 T scanners using scanner specific protocols. Briefly, DTI data were acquired with a voxel size of 1.372 × 2.70 mm3, 41 diffusion gradients and a b-value of 1000 s/mm2. IR-SPGR data were acquired with a voxel size of 1.022 × 1.20 mm3.
AV45 and fludeoxyglucose (FDG-PET) imaging data were acquired on several types of scanners using different acquisition protocols. In order to increase data uniformity, the data underwent a standardized preprocessing procedure at the ADNI project.
All imaging protocols and preprocessing procedures are available at the ADNI website (http://adni.loni.usc.edu/methods/).
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6

Cortical Thickness Measurement in MRI

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All MRI were performed using General Electric 3T scanners with a three‐dimensional T1‐weighted Magnetization Prepared Rapid Acquisition Gradient Echo sequence. Regional cortical thickness measurements were estimated using FreeSurfer 5.3 software with default settings.33 Cortical thickness measures were estimated for the following: temporal (entorhinal, parahippocampal, banks of superior temporal sulcus, fusiform, inferior temporal, insula, middle temporal, superior temporal, temporal pole, transverse temporal), frontal (regions of interest [ROIs] from caudal middle frontal, frontal pole, lateral orbitofrontal, medial orbitofrontal, pars opercularis, pars orbitalis, pars triangularis, rostral middle frontal, superior frontal), and parietal (ROIs from inferior parietal, precuneus, superior parietal, supramarginal).34
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7

Multi-Modal Brain Imaging Protocol

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DWI, FLAIR, and inversion-recovery spoiled gradient recalled (IR-SPGR) T1-weighted imaging data were acquired on several General Electric 3T scanners using scanner specific protocols. Briefly, DWI data was acquired with a voxel size of 1.372 × 2.70 mm3, 41 diffusion gradients, and a b-value of 1,000 s/mm2 using an echo-planar imaging sequence with a 90° flip angle. T1-weighted data were acquired using a gradient-echo sequence with an 11° flip angle and a voxel size of 1.022 × 1.20 mm3.
AV45 PET imaging data were acquired on several types of scanners using different acquisition protocols. To increase data uniformity, the data underwent a standardized preprocessing procedure at the ADNI project. All imaging protocols and preprocessing procedures are available at the ADNI website2.
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8

Resting-State fMRI and Language Mapping in Presurgical Workup

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Each patient received resting state fMRI scan as part of the routine presurgical workup. Scanning was performed on 3-T scanners (GE Healthcase, Milwaukee, Wisconsin) using an eight-channel head coil. For task based and rsfMRI, T2*-weighted images were acquired with a single-shot gradient echo echo-planar imaging (EPI) sequence in the axial orientation (repetition time/echo time (TR/TE) = 2500/30 ms, flip angle = 80°, slice thickness = 4 mm, field-of-view (FOV) = 240 mm2, matrix = 64×64) covering the whole brain. Three-dimensional T1-weighted images were acquired with a spoiled gradient recalled sequence (TR/TE = 22/4 ms, matrix = 256 × 256 matrix, flip angle = 30°, slice thickness = 1.5 mm). For the resting state fMRI scan, patients were instructed to leave their eyes open, focus on looking at a crosshair, and not think about anything during the scan. A total of 160 volumes were acquired. Of the 51 patients included in the study, 40 also performed a silent word generation task in the same session as part of presurgical language mapping. The language tasks were used to determine language laterality (right dominant, left dominant or bihemispheric dominance) using methodology previously used in Dong et al. and was documented in the patients final presurgical mapping report18 (link).
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9

Multiband EPI fMRI Protocol for MID Task

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Multiband echo-planar imaging (EPI) fMRI volumes were acquired during the MID task. Acquisition parameters were harmonized to allow collection on Philips, Siemens and GE 3 T scanners. Main EPI parameters were: 90 × 90 matrix, 60 slices, 216 × 216 field of view, TR = 800 ms, TE = 30 ms, flip angle = 52°, multiband factor = 6 and voxel size = 2.4 × 2.4 × 2.4 mm. For more details on the imaging acquisition protocol, including the anatomical scan, see Casey et al. (B. Casey et al., 2018 (link)).
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10

Functional MRI Acquisition Protocol

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Data were collected using an 8-channel head coil on one of two 3T scanners (GE Medical Systems, Milwaukee, WI): a Signa HDx (TR = 2000 ms, TE = 30 ms, flip angle = 80°, 64×64 matrix, ASSET factor = 2, 40 2.6-mm axial slices with a 0.4-mm gap, 244 volumes) and a Discovery MR750 (TR = 2000 ms, TE = 30 ms, flip angle = 80°, 64×64 matrix, ASSET factor = 2, 40 3.0-mm axial slices, 244 volumes). The first four volumes of each run were discarded to discount T1 saturation. Field maps were acquired to correct for susceptibility-induced geometric distortions. High-resolution T1-weighted fast spoiled gradient echo (FSPGR) anatomical images (Signa HDx: TR = 7.7 ms, TE = 2.98 ms, flip angle = 8°, 192×256 matrix, 172 1-mm slices; MR 750: TR = 8.1 s, TE = 3.17 ms, flip angle = 8°, 256×256 matrix, 172 1-mm slices) were obtained sagittally for spatial normalization and activation localization.
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