Achieva 3t mri system

Scans were acquired with a Philips Achieva 3T MRI system. A T1-weighted structural scan was acquired at the beginning of the scan session, followed by three functional gradient-echo EPI scans with axial orientation (30 slices with 3 mm inplane resolution and 0.5 mm gap, 2 s TR, 25 ms TE, 79° flip angle, A-P phase-encode direction). A single TR EPI scan with opposite phase-encoding direction (P-A), but otherwise identical to those above, was acquired for use in correcting geometric distortions. Each subject underwent a single scanning session, lasting approximately one hour (the scan session also included acquisition of spectroscopy data for a separate experiment). When possible, subjects’ eyes were tracked during scanning using an Eyelink 1000 Plus eyetracker, sampling at 1000 Hz. Due to the challenges of eyetracking in the scanner, we were able to collect data for 55% of subjects (N(NT)=17, N(ASD)=9). We found no group differences in eye movement behavior in the subjects whose eyes were successfully tracked. We found no difference in the proportion of time spent fixating (t₂₄ = −0.62, p=0.54), or the mean (t₂₄ = −1.18, p=0.25) or standard deviation (t₂₄ = −1.20, p=0.24) of the distance of eye position from the fixation mark.

MRI scans were collected using an Achieva 3 T MRI system (Philips Healthcare). Structural MRI (sMRI) data of one volume were acquired in coronal planes with a 3D T1‐weighted SENSE parallel imaging sequence: number of slices = 210, slice thickness = 1.00 mm, matrix size = 256 × 256, and in‐plane resolution = 0.875 mm × 0.875 mm. Resting state fMRI (rsfMRI) data of 165 volumes were obtained in axial planes with a T2*‐weighted gradient‐echo echo‐planar imaging sequence: repetition time = 2,000 ms, echo time = 30 ms, number of slices = 31, slice thickness = 4.00 mm, matrix size = 80 × 80, and in‐plane resolution = 2.75 mm × 2.75 mm. Using the tools in SPM12 (http://www.fil.ion.ucl.ac.uk/spm/, RRID:SCR_007037) and DPARSF (http://rfmri.org/DPARSF/, RRID:SCR_002372), sMRI and rsfMRI data were preprocessed. GM volume, as a main measure indicating structural abnormalities in PD and AP, was acquired from sMRI. In addition, as measures representing functional abnormalities at local and global levels, regional homogeneity (ReHo) (Zang, Jiang, Lu, He, & Tian, 2004) and degree centrality (DegCen), respectively, were obtained from rsfMRI. Details on how the neuroimaging data were processed to acquire the structural and functional measures are described in Appendix S1.

Using an Achieva 3 T MRI system (Philips Healthcare, Best, Netherlands), structural MRI (sMRI) and diffusion-weighed MRI (dMRI) data were collected for the individuals. For sMRI data, a T1-weighted volume image was acquired in axial planes with the following parameters: number of slices = 124, slice thickness = 1.60 mm, matrix size = 512 × 512, and in-plane resolution = 0.47 mm × 0.47 mm. For dMRI data, 46 volume images comprising 45 with diffusion weighting at b value = 1,000 s/mm² and one without diffusion weighting were acquired in axial planes with the following parameters: number of slices = 60, slice thickness = 2.25 mm, matrix size = 112 × 112, and in-plane resolution = 1.96 mm × 1.96 mm.
Preprocessing of the dMRI data was conducted using tools in FSL¹ in such a way that eddy current-induced distortion and head movement were corrected and the skull was removed before modelling the diffusion tensor at each voxel. White matter (WM) tractography was performed for the preprocessed dMRI data to reconstruct WM fibers over the whole brain by using tools in MRtrix3.² For registration between the dMRI native space and the standard space, a deformation field was estimated for the sMRI data coregistered to the dMRI data by using tools in SPM12.³