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"copy_inputs_flywheel" downdloads the scans from flywheel and does preprocessing. Perform n4 correction first. Then create manual raw-to-axisalign affine transformation. This script contains the function to apply the affine transform to n4 corrected scans.
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"organize_inputs" organizes the data required for atals construction in a preproc directory
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"build_mst_srlm_atlas2022" is the main script for constructing the atlas.
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"reslice_histo_segs" maps the histology annotations from subject space to the template and computes the consensus segmentation
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tau_density_to_atlas maps the NFT burden maps from subject space to the templae and computes the average maps and ROI measures
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template_skel_analysis contains the thickness computation and meshglm analyses for surface based analyses
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Scripts for constructing the ex vivo MRI atlas and mapping annotations and tau burden maps from histology
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