Computational protocol: Functional connectivity in dementia with Lewy bodies: A within‐ and between‐network analysis

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Protocol publication

[…] A first preprocessing step was carried out using FEAT (FMRI Expert Analysis Tool) Version 6.0 which is part of the FMRIB's software library (FSL, http://www.fmrib.ox.ac.uk/fsl) including motion correction using FMRIB's Linear Image Registration Tool (MCFLIRT), slice‐timing correction, and spatial smoothing with a 6.0mm full width at half maximum Gaussian kernel. Participants were excluded if the MCFLIRT‐estimated motion parameters exceeded 2 mm translation and/or 2° rotation. To assess differences in movement between the three groups due to patients with Parkinsonian symptoms the following formula was used (Liao et al., ): head motion/rotation=M−1−1∑i=2Mxi−xi−12−yi−yi−12−zi−zi−12,where M is the total number of volumes (M = 128) and xi, yi, and zi are the translations/rotations at the ith time point in x, y, and z direction.Denoising was performed with ICA‐AROMA in FSL which performs single‐subject independent component analysis (ICA) to remove motion components from each participant's functional data (Pruim, Mennes, Buitelaar, & Beckmann, ; Pruim et al., ). Additionally, eroded CSF and white matter masks were estimated using FAST in FSL and the mean signal inside the mask was regressed out of each participant's cleaned functional data. Functional and structural images were then co‐registered using boundary based registration in FSL, and normalized to the standard MNI template using Advanced Normalization Tools (Avants et al., ; Klein et al., ). Finally, functional data were temporally high‐pass filtered with a cutoff of 150 s and resampled to a resolution of 4 × 4 × 4 mm3. Grey matter probability maps were obtained from the FAST‐segmented T1 images and included as voxel‐wise spatial covariates in the group comparison analyses. […]

Pipeline specifications

Software tools FreeSurfer, ANTs
Application Functional magnetic resonance imaging
Organisms Homo sapiens
Diseases Alzheimer Disease, Dementia, Parkinson Disease, Secondary, Lewy Body Disease