Computational protocol: Multiple non-cell-autonomous defects underlie neocortical callosal dysgenesis in Nfib-deficient mice

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Protocol publication

[…] Following perfusion fixation and phosphate-buffered saline washing, diffusion-weighted images were acquired with the samples immersed in Fomblin Y-LVAC fluid (Solvay Solexis, Italy), using a 16.4 Tesla Bruker scanner and a 10 mm quadrature birdcage coil. A three-dimensional diffusion-weighted spin-echo sequence was acquired using a repetition time of 400 ms, an echo time of 22.8 ms and an imaging resolution of 0.08 × 0.08 × 0.08 mm with a signal average of 1. Each dataset was composed of two Bo and thirty direction diffusion-weighted images (b value of 5,000 s/mm2, δ/Δ = 2.5/14 ms). Reconstruction and tractography were performed with Diffusion Toolkit [] according to high angular resolution diffusion (HARDI) and Q-ball models []. Tractography limits were set at fractional anisotropy values greater than 0.1 and a turning angle ≤ 45°. Hippocampal commissure tractography was performed using hand-drawn regions-of-interest on colour-coded fractional anisotropy maps in TrackVis []. […]

Pipeline specifications

Software tools DTK, TrackVis
Applications Magnetic resonance imaging, Diffusion magnetic resonance imaging analysis
Organisms Mus musculus, Homo sapiens
Diseases Callosities, Deficiency Diseases