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Homogenates of infectious brains were generated using a rhybolyzer in a biosafety level 3 laboratory.
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Surface mesh representations of the head were generated using Brain Voyager and vectors linking key anatomical landmarks were drawn on the mesh.
A standard brain was generated using CMTK software to average six male and female brains stained with nc82 (anti-Bruchpilot) that were of good quality (Rohlfing and Maurer, 2003; Rohlfing, 2012).
Low magnification images of entire brain sections were generated using an Axioscan Z1 (Carl Zeiss, Göttingen, Germany) slide scanner.
Confocal microscope images of various brain regions were generated using either the 63× objective and the Zeiss LSM 510 Meta or the 2× objective on the Olympus BX61.
First, the polygon mesh models of the scalp and brain surface were generated using the Marching cube method (Lorensen and Cline 1987).
Volumetric analysis was performed using voxel-based morphometry (VBM8), and 116 cortical and subcortical brain regions were generated using the Automated Anatomical Labeling (AAL) atlas (Grieve et al., 2013a, Tzourio-Mazoyer et al., 2002).
Tractography-based connectivity estimates between injection site ROIs and targets from the ABA mouse brain anatomic segmentation were generated using the previously described methods.
To examine which cortical regions showed a greater blood oxygen level dependent (BOLD) response to the various trial types in the main experiment, full-brain statistical parametric maps were generated using an uncorrected voxel-level threshold of P < 0.001 and a cluster size threshold of 6 voxels resulting in a corrected threshold of P < 0.05.
Whole-brain thalamic functional connectivity maps were generated using individual subjects' anatomically defined thalamic seeds.
Automated outlines of brain areas classified as 'abnormal' were generated using Seghier et al. 's (2008) modified segmentation-normalization procedure.
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