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Chunk #5 — Acquisition methods

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Layer-dependent functional connectivity methods.
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All functional data were acquired with VASO contrast (Hua et al. 2013; Huber et al. 2014b; Lu et al. 2003) and a 3D-EPI readout (Poser et al. 2010). Slab-oversampling was applied in the second phase direction. 3D slice aliasing was minimized by using a sharp slab-excitation pulse profile with a bandwidth-time-product of 25. The readout parameters were: in-plane FLASH GRAPPA 3 (Talagala et al. 2016), with regularization strengths chi = 1–5000 (for instructions how to do this, see here: https://layerfmri.com/grappa-regularization/), TE = 25 ms, partial Fourier = 6/8 with POCS reconstruction of 8 iterations. Online reconstruction was performed using a GRAPPA kernel size 6 × 5 × 3. Resolutions of fMRI protocols varies between 0.5 × 0.5 × 0.6 and 0.8 × 0.8 × 0.8 mm3. For anatomical reference, 3 averages of 0.5 mm iso MP2RAGE data with partial brain coverage were acquired. For optimal use in layer-fMRI (https://layerfmri.com/mp2rage), background noise (outside the brain) was minimized with a regularization term lambda = 0.1, fold-over-artifacts were minimized by using an excitation pulse BWTP of 25, and no partial Fourier was applied