Computational protocol: Altered functional connectivity of the amygdaloid input nuclei in adolescents and young adults with autism spectrum disorder: a resting state fMRI study

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Protocol publication

[…] All image preprocessing and analyses were performed using FSL (FMRIB Software Library, http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/) []. The following pre-statistical processes were applied to the fMRI data: nonbrain removal using Brain Extraction Tool (BET); rigid-body motion correction using MCFLIRT; high-pass temporal filtering (Gaussian-weighted least-squares fitting with frequency cutoff point = 100 s); correction of off-resonance geometric distortions in the EPI data using PRELUDE and FUGUE, using B0 field maps derived from the dual-echo gradient echo dataset; artifact removal based on probabilistic ICA (Independent Component Analysis) using MELODIC; spatial normalization to Montreal Neurological Institute (MNI152) 2 mm isotropic atlas space using boundary-based registration (BBR); and FNIRT and Gaussian filtering (full width at half maximum (FWHM) = 6 mm; see the the “Statistical analysis” section). The dual-echo images (TE = 16 and TE = 36) were combined by averaging both echo times. We excluded one participant with ASD due to excessive head movement in terms of frame-wise displacement (max. frame-wise displacement (FD) = 8.7 mm, Mfd = 0.89 mm), resulting in 20 datasets from the ASD group and 25 datasets from the control group for further analysis (see Additional file for relative frame-wise displacement). To rule out the possibility that differences in movement between the ASD and control group could contribute to the results, we calculated the mean value of frame-wise movement (i.e., the movement of one TR relative to previous TR) for each participant and compared it between the two groups. No group difference was found (Masd = 0.10, SDasd = 0.10; Mctrl = 0.07, SDctrl = 0.42; t(25) = 1.73, p = 0.1). […]

Pipeline specifications

Software tools FSL, BET
Applications Magnetic resonance imaging, Functional magnetic resonance imaging
Diseases Liver Diseases