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80 protocols using spm12

1

Preprocessing and Analysis of fMRI Data

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Preprocessing and statistical analysis of the image data were done using SPM12 (SPM12/">www.fil.ion.ucl.ac.uk/spm/software/SPM12/, accessed 27 July 2020) executed in MATLAB version 8.5 (R2015a) (www.mathworks.com, accessed 27 July 2020). To account for movement of the subject, all fMRI image volumes were realigned to the first volume of the corresponding session and subsequently coregistered to the corresponding structural T1 image using rigid-body transformation. A Volterra expansion was performed on the generated six realignment parameters to model residual movement artefacts (Lund et al., 2005 (link)) resulting in 24 movement parameters, which were later entered into the design matrix as regressors of no interest.
For the T1 image, the origin was set to the AC–PC plane and the images were segmented using the SPM12 segmentation procedure. The produced normalization parameters were then applied to all coregistered fMRI image volumes. Successful normalization to standard Montreal Neurological Institute (MNI) coordinate space was checked at random for each subject using ventricles and brain borders as landmarks. Finally, all fMRI image volumes were smoothed with an isotropic 8-mm full width half maximum Gaussian filter.
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2

FDG-PET Image Preprocessing and Normalization

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FDG-PET data were pre-processed and analyzed using SPM12 (SPM12">www.fil.ion.ucl.ac.uk/spm/software/SPM12) in Matlab (MathWorks, Inc.). The averaged FDG-PET images of frame 3–6 were first aligned horizontally along the anterior and posterior commissure and co-registered to structural MRIs. Spatial normalization to MNI space was performed using the FDG-PET template (available as an SPM extension), while keeping the original voxel size. Normalized image dimensions were 128/155/128 (x/y/z). For spatial smoothing, a 6 mm full-width at half-maximum (FWHM) Gaussian filter was applied, with filter size selected according to the high-spatial resolution.
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3

Neuroimaging Analysis of MRI Data

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DICOM images from the MRI were converted to NIfTI format using conversion software dcm2niix (https://github.com/rordenlab/dcm2niix/releases, accessed on 25 February 2022 Computational image processing of T1-weighted images was performed using voxel-based morphometry (VBM) [43 (link)]. The processes were carried out with SPM12 (SPM12/">https://www.fil.ion.ucl.ac.uk/spm/software/SPM12/, accessed on 25 February 2022 ) in a MATLAB 2017b environment (developed by the MathWorks, Inc., Natick, MA, USA) utilizing the cluster service UBELIX (https://ubelix.unibe.ch, accessed on 25 February 2022) from the University of Bern, Switzerland. ‘fsleyes’ from FSL (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki, accessed on 25 February 2022) served as the viewing software for qualitatively assessing the scans and interpreting the results.
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4

fMRI Data Analysis with SPM12 and BIDS

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fMRI data analysis was performed using Matlab (version R2014b 8.4.0, RRID:SCR_001622, The MathWorks) and SPM12 (RRID:SCR_007037, SPM12/">www.fil.ion.ucl.ac.uk/spm/software/SPM12/). Raw data was imported according to BIDS standards (RRID:SCR_016124, http://bids.neuroimaging.io/), and was then unwarped, realigned and slice time corrected.
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5

Evaluating Image Quality in Multimodal Imaging

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We visually evaluated the image quality of MR and PET images (fxPET and cPET) based on the consensus decisions of two radiologists using a four-point scoring system.
Regarding MR images (T1WI and T2WI), we evaluated overall image quality using the following four-point score: 0 = poor (non-diagnostic quality); 1 = fair (low quality with distinct artifacts and strong noise); 2 = good (satisfactory quality with few artifacts or moderate noise); and 3 = excellent (no artifacts and low noise).
Regarding PET images, we evaluated overall image quality and sharpness considering artifact and noise (Table 1). For 12 patients with intracranial lesions, we examined the number of detected lesions and the subjective contrast of those lesions. We defined lesions as areas showing focal 18 F-FDG uptake that was increased or decreased compared with background physiological uptake in the brain.
Quantitative evaluation: registration accuracy and regional 18 F-FDG uptake accuracy For evaluation of registration accuracy and regional 18 F-FDG uptake accuracy, we measured the spatial coordinates and regional standardized uptake value (SUV), using SPM12 (https://www.fil.ion.ucl.ac.uk/spm/software/SPM12), MATLAB (R2016b, MathWorks, Natick, Massachusetts, Untied States) and ImageJ software (National Institutes of Health, Bethesda, Maryland, United States).
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6

Voxel-Based and Surface-Based Neuroimaging Analysis

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Data for Voxel-Based Morphometry were preprocessed and analyzed with SPM12 (SPM12/">http://www.fil.ion.ucl.ac.uk/spm/software/SPM12/) [33 (link)–35 (link)] running under MATLAB R2018b (https://www.mathworks.com/products/new_products/release2018b.html). For surface-based feature extraction, we used FreeSurfer 5.3.0 (http://surfer.nmr.mgh.harvard.edu [36 (link),37 (link),]). Quality control was performed using standardized ENIGMA quality control procedures (http://enigma.ini.usc.edu/protocols/imaging-protocols/).
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7

Preprocessing Pipeline for Structural and Functional MRI Data

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Data were preprocessed using SPM12 (www.fil.ion.ucl.ac.uk/spm), automated in Matlab (version 8.0.0.783 R2012b; The MathWorks) with Automatic Analysis (AA) 5.0 (Cusack et al., 2015 (link); https://github.com/rhodricusack/automaticanalysis). T1 anatomical images for each participant in each visit were coregistered to the Montreal Neurological Institute (MNI) template using rigid-body transformation, bias corrected, and segmented by tissue class. Diffeomorphic registration was then applied across participants separately for each visit to the gray matter to create a group template using DARTEL (Ashburner, 2007 (link)), which was in turn affine transformed to MNI space. EPI distortions in the functional images were corrected using field maps. Next, the images were corrected for motion and then for slice acquisition times by interpolating to the 26th slice in time. The images were rigid-body coregistered to the corresponding T1 image and transformed to MNI space using the diffeomorphic + affine transformations. These normalized images were then smoothed by 6 mm FWHM.
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8

Preprocessing RS-fMRI Data with DPABI

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All RS‐fMRI data were preprocessed using DPABI (Yan & Zang, 2010 (link)) based on MATLAB (https://www.mathworks.com/) and SPM12 (https://www.fil.ion.ucl.ac.uk/spm/) with the following procedures: removing the first 20 s of the brain volumes, slice time correction, motion correction, spatial normalization via nonlinear registration to an EPI template with a resampling resolution of 3 × 3 × 3 mm, and spatial smoothing with a Gaussian kernel of 6 mm in three directions. The Friston 24‐parameter model (Friston et al., 1996) was used to reduce the potential effect of head motion, and the averaged time courses of cerebrospinal fluid (CSF) and white matter were considered nuisance variables and were regressed out from each voxel's time series using a multiple regression model.
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9

Neuronal Correlates of Controllability

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Images were collected using a 3 T Siemens Prisma Scanner with a 64-channel head coil. The neuroimaging data were analyzed using SPM12 (the Wellcome Trust Centre for Neuroimaging, London, UK; SPM12/">http://www.fil.ion.ucl.ac.uk/spm/software/SPM12/), running under MATLAB R14a (MathWorks Inc., Natick MA, USA). Our analysis included a standard pre-processing procedure (spatial realignment, coregistration, normalization and smoothing) and general linear modeling. We used region of interest (ROI) analyses; to this end, we selected a priori ROIs based on previous literature on neuronal underpinnings of controllability and created a combined mask containing these ROIs using Marina (http://www.bion.de/eng/MARINA.php) to correct for α-error accumulation associated with testing multiple ROIs. We additionally used a psychophysiological interaction (PPI) analysis as implemented in SPM12 to assess controllability-dependent connectivity changes between the vmPFC and the amygdala as the vmPFC–amygdala cross talk is assumed to play a critical role in the reduction of fear (Milad and Quirk, 2002 (link); Bouton et al., 2006 (link); Adhikari et al., 2015 (link)).
A more detailed description of the experimental procedure, behavioral analyses, skin conductance and imaging analyses is provided in the supplemental material.
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10

Neuroimaging of Depression Recovery

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Analysis of imaging data was performed in SPM12 and Matlab R2012 (Mathworks, Sherborn, MA). We calculated group-wise comparisons (AN versus HC, REC versus HC and vice versa) applying SPM-t-contrasts. Age and total intracranial volume (TIV) were respected as covariates to exclude confounding effects. We applied a statistical threshold of p < 0.05 after family-wise error (FWE) correction.
In a further analysis, the BDI-II (35 (link), 36 ) was added as a covariate to correct for the influence of depressiveness.
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