The AS-NoSOD group (N = 27) presented normal speech onset, whereas the AS-SOD group (N = 28) was characterized by a SOD.

AS individuals (N = 55)

SPSS

Brain Connectivity Toolbox

Automated Anatomical Labeling Atlas (AAL)

The FA threshold of 0.15

Each line was propagated by 0.25 mm to the next point in space, at which point the process was repeated. Each of these streamlines was terminated when FA < 0.15 or when the angular deviation from paths was >55° to prevent streamlines from looping back

Deterministic tractography was performed using the Diffusion Toolkit in PANDA, a MATLAB

FSL's “dtifit” tool

“auto_warp” command in AFNI

“fsl_prepare_fieldmap” tool in FSL

skull-stripped using the Brain Extraction Tool

“eddy” tool from FSL

Diffusion tensor imaging data was acquired using a single-shot spin echo echo-planar imaging (EPI) sequence with 30 gradient directions and the following acquisition parameters: repetition time (TR) = 7700 ms; echo time (TE) = 90 ms; b = 1000 s/mm2; acquisition matrix = 204 × 204; voxel size = 2.0 × 2.0 × 2.0 mm, 60 contiguous axial slices and scan time = 8 min 22 s. High-resolution T1-weighted structural images were also acquired by collecting 176 contiguous sagittal slices using a three-dimensional magnetization prepared rapid gradient echo imaging (3D MPRAGE) sequence with the following parameters: repetition time (TR) = 2250 ms; inversion time (TI) = 850 ms; echo time (TE) = 3.98 ms; field of view (FOV) = 256 mm; acquisition matrix = 256 × 256; voxel size = 1.0 × 1.0 × 1.0 mm; slice thickness = 1.0 mm; flip angle = 9°. A field map was also recorded with a gradient echo sequence with the parameters of repetition time (TR) = 488 ms; echo time 1 (TE 1) = 4.92 ms; echo time 2 (TE 2) = 7.38 ms; voxel size = 3.0 × 3.0 × 3.0 mm; field of view (FOV) = 204 mm; slice thickness = 3.0 mm; 40 slices; flip angle = 60° to measure field inhomogeneities and compensate for geometrical distortions that result from standard EPI sequences.

3 T Siemens Trio MRI scanner using a 12-channel head coil

The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.

GWCi = β0 + β1Gj + β2 agej + β3 agej2 + β4 agej3 + β5 (agej × groupj) + β6 (agej2 × groupj) + β7 (agej3 × groupj) + β8 IQj + εi, where ε denotes the residual error.

Corrections for multiple comparisons across the whole brain were performed using random-field theory (RFT)-based cluster-corrected analysis for non-isotropic images using a p < 0.05 (two-tailed) cluster-significance threshold

F-test for nested model comparisons was performed at each vertex

linear, quadratic, and cubic effects of age, in addition to the main effect of group in a vertex-wise fashion

SurfStat toolbox (http://www.math.mcgill.ca/keith/surfstat/) for Matlab (R2016a; www.mathworks.com)

smoothed using a 10-mm full-width at half-maximum (FWHM) surface-based Gaussian kernel prior to statistical analyses

final sample size of 153 participants (n = 77 individuals with ASD and n = 76 TD controls)

FreeSurfer v5.3.0

3-Tesla GE Signa System (General-Electric, Milwaukee, WI) with full-head coverage, 196 contiguous slices (1.1-millimetre (mm) thickness, with 1.09 × 1.09 mm in-plane resolution), a 256 × 256 × 196 matrix, and a repetition time/echo time (TR/TE) of 7/2.8 milliseconds (ms) (flip angle = 20°, FOV = 28 cm). A (birdcage) head coil was used for radiofrequency transmission and reception.

aged 7 to 25

Eighty-two (82) right-handed males with ASD and eighty-two (82)

support the connections among research networks, rather than supportingfundamental research as the primary activity

NSF Big Ideas

These data are obtained from the Human Connectome Project and thus we must adhere to their data use terms (https://www.humanconnectome.org/study/hcp-young-adult/data-use-terms). They provide data access at the following link: https://db.humanconnectome.org/.

independent samples t-tests and analyses of covariance (ANCOVAs; controlling for age and ICV) to test for gender differences in FFM traits and amygdala/hippocampal volumes, respectively

Hippocampal subfield segmentation was derived using the automated algorithm available in FreeSurfer version 6.0

a modified version of the FreeSurfer automated “recon-all” pipeline

Chris Rorden’s DICOM to NIFTI

8 participants did not complete the NEO-FFI

1,113 participants

Data were drawn from the publicly available repository of the WU-Minn HCP

Human Connectome Project sample (N = 1105)

FreeSurfer amygdala and hippocampus segmentation pipelines

The raw data supporting the conclusions of this manuscript will be made available by the authors, without undue reservation, to any qualified researcher.

covariates

Inferential statistics on the clinical variables were performed with SPSS v24

All the statistics were performed with SPM12 using a threshold p < 0.05 corrected for the False Discovery Rate (FDR) at voxel level.

The ARtifact Detection Tool (ART) was employed to create regressors and detect outliers

FWHM equal to 6 mm

final voxel size of 2 × 2 × 2 mm3

pre-processed using SPM12 (49) and ANTs

FA, MD, AD, and RD with a GLM comparing HCs and FRDA patients while accounting for age and sex as covariates

JHU DTI-based WM atlas

Voxel-wise statistics were performed for each DTI derived map with a general linear model (GLM) using age and sex as covariates, with the same approach previously described for VBM

DTI-TK

Tortoise

Voxel-wise statistics were computed with a general linear model (GLM) using FSL (41), with age, sex, and intracranial volume (ICV) in native space as covariates.

FSL anatomical pipeline

pre-processed with the N4 tool of ANTs

Voxel-Based Morphometry (VBM) pipeline

Instructors: J. Bates, S. Ghosh, J. Grethe, Y. Halchenko, M. Hanke, C. Haselgrove, S. Hodge, D. Jarecka, D. Keator, D. Kennedy, M. Martone, N. Nichols, S. A. Abraham, J.-B. Poline, N. Preuss, M. Travers, and others

IBM SPSS Statistics,

FSL (version 5.0.7)

FSL and Freesurfer software

(VBM) protocol, using the default pipeline as implemented in FSL

94 AD

217 MCI

145 CTRL

Controls and patients aged 60 years or older and from both genders, were included prospectively during 2015–2016 (n = 44). AD patients

cognitively normal individuals paired by age (n = 16)

3T whole-body MRI systems (Magnetom TIM Trio; VB17 software version; Siemens Healthcare):

MPM sequence

We used a backtracking algorithm (55) to parcellate 66 regions defined by sulcogyral criteria in the Desikan–Killiany atlas (56) into 308 contiguous parcels of approximately equal area (500 mm2) across both hemispheres in standard space (SI Appendix, Fig. S2A).

FreeSurfer v5.3.0

sample of 297 healthy young people sampled from primary healthcare registers, stratified by age, and balanced for sex in the adolescent age range 14–24 y old, with ∼60 participants in each of five age-defined strata: 14–15 y old inclusive, 16–17 y old, 18–19 y old, 20–21 y old, and 22–24 y old

that adolescent consolidation of these connectome hubs was associated with a specific gene expression profile, enriched for neuronal and oligodendroglial function, and enriched for risk of schizophrenia, a neurodevelopmental disorder with its highest incidence in young adults

(ii) that adolescent cortical shrinkage/myelination (also known as consolidation) was concentrated anatomically on association cortex and topologically on the most strongly connected regions (hubs) of the human brain anatomical network

(i) that adolescent cortical shrinkage was coupled to intracortical myelination

The age, MMSE, HAMD,and HAMA were performed with independent samples T test, and sex was performed with Chi-Square test.

Significant difference was set at a P value of <0.05

PASW Statistics 18.0

ITK-SNAP (V3.6.0)

visually inspected to confirm anatomical accuracy

the new segment tool embedded in SPM 12 software

rest software

WMH volume was examined as a percentage of166ICV

adjusted for age159and

3dRegAna, AFNI

sigma 2 mm

Voxelwise GM density was calculated using the145standard FSL VBM package

subject’s age, sex, and eTIV were considered in the matrix design in the SPM12

extent threshold was set at 250 voxels

SPM12 using an uncorrected threshold of p < 0.001

Statistical Package for Social Sciences software ver. 16.0

p-value of less than 0.05 was used for group comparisons, and the extent threshold was set at 50 voxels

SPM12

adjusted for estimated total intracranial volume (eTIV) and age

FreeSurfer

5.3.0

8-mm full-width-half-maximum Gaussian smoothing kernel

SPM12

MRICRON

VBM technique implemented in the CAT toolbox

NIfTI

For investigating group differences, we run voxel-wise linear regression in the form:X~A + βgroupGroup + βageAge + βsexSex + βscan−chScan − ch + βintervalInterval + βICVICV + εwhere X is the Jacobian determinant value at a given position, A is the constant Jacobian determinant term, the βs are the covariate regression coefficients, and ε is an error term.

ANTs Symmetric Normalization (SyN; (Avants et al., 2008))

flirt (http://fsl.fmrib.ox.ac.uk)

Brainsuite (http://brainsuite.org)

(http://www.itksnap.org)

SPSS version 20.0

Student’s t-test.

FreeSurfer 5.1.0

Inbrain®, a Korea Food and Drug Administration (KFDA)-cleared software and a registered trademark of MIDAS Information Technology Co., Ltd., which performs fully-automated image analysis of brain structures

Brain regions showing a significant interaction between group and Eyes Test score in the association with gray matter volume

1.5 × 1.5 × 1.5 mm and smoothed using a 12-mm full-width at half-maximum (FWHM) isotropic Gaussian kernel

SPM81 and the VBM8 toolbox2 implemented in MATLAB R2012b

analyzed using a t-test between groups and analysis of covariance (ANCOVA) with group (TD and ASD) as an effect-of-interest factor and age, sex and full-scale IQ as effect-of-no-interest covariates. A p-value < 0.05 was considered significant.

SPSS 16.0J

we performed PLS (McIntosh et al., 1996) using PLSGUI7

probabilistic cytoarchitectonic atlas included in the SPM Anatomy toolbox

Automated Anatomical Labeling atlas (Tzourio-Mazoyer et al., 2002) included in the MRIcron software

significance in both of these parametric and nonparametric analyses are reported. We also explored the effects of ASD subtype (Asperger’s disorder vs. PDD-NOS) using these predefined thresholds. The clusters that showed significant group difference (TD > ASD) were used as an inclusive mask.

Permutation Analysis of Linear Models software

VBM using a general linear model analysis, with group as the effect-of-interest factor and sex and age as the effect-of-no-interest covariates. The association between group difference and the volume of the gray matter was tested using T-statistics and reported as a Z-score after the T-value was transformed into the standard normal distribution. Voxels were deemed to be statistically significant if they reached the extent threshold of p < 0.05, after false-discovery rate (FDR) correction for multiple comparisons based on the topological FDR procedure (Chumbley and Friston, 2009), with a cluster-forming threshold (CFT) of p < 0.01 (uncorrected)

with default settings

visual inspection of T1 images and confirmed no macroscopic lesions or artifacts in the images

VBM8 toolbox

MATLAB R2012b

MarsBaR toolbox

GingerAle

Statistical Non-Parametric Mapping toolbox

age as a covariate and the results were assessed on the basis of nonparametric cluster-wise inference, with a cluster-forming threshold of 0.005 and cluster-based correction for multiple comparisons such that pFWE < 0.05. In addition, we re-ported any results passing the cluster-forming threshold of p < 0.005

GingerAle

Anatomic Labelling (AAL) system in the WFU pickatlas (www.nitrc.org/projects/wfu_pickatlas/).

controlling for age

MarsBaR toolbox (http://marsbar.sourceforge.net/)

Statistical Non-Parametric Mapping toolbox (http://warwick.ac.uk/snpm), with a cluster-forming threshold of 0.005 and a family-wise error (FWE) of 0.05

included age as a covariate

Neurosynth software (neurosynth.org) to conduct a reverse inference meta-analysis of previously published studies with the predefined search term “theory mind.”

smoothed with an iso-tropic 8 mm full-width at half-maximum

final voxel size of 1.5 × 1.5 ×1.5  mm3; segmentation into grey matter, white matter and cerebrospinal fluid; and modulation by the nonlinear com-ponent only for volume changes during spatial normalization to identify regional differences in grey matter volume cor-rected for individual brain size

MATLAB 2014

SPM8

VBM

IBM SPSS Statistics® version 22.

z-distribution Monte Carlo simulation with 10,000 repeats was then applied to correct for multiple comparisons using a cluster-forming threshold set at p < .05.

FreeSurfer version 6.0

3D MP-RAGE sequence (TR/TE:2300/3.03 ms; flip angle: 90; 192 sagittal slices with 1 mm3 voxel size

3 T Siemens Skyra scanner with a 20-channel head coil

Workshop Details August 20 – September 4, 2016 Friday Harbor Laboratories

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