Scripts for building the 3D ex vivo MRI atlas

Scripts

"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.
"organize_inputs" organizes the data required for atals construction in a preproc directory
"build_mst_srlm_atlas2022" is the main script for constructing the atlas.
"reslice_histo_segs" maps the histology annotations from subject space to the template and computes the consensus segmentation
tau_density_to_atlas maps the NFT burden maps from subject space to the templae and computes the average maps and ROI measures
template_skel_analysis contains the thickness computation and meshglm analyses for surface based analyses

Name		Name	Last commit message	Last commit date
Latest commit History 4 Commits
README.md		README.md
build_mst_srlm_atlas2022.sh		build_mst_srlm_atlas2022.sh
calculate_label_thk.R		calculate_label_thk.R
common.sh		common.sh
compute_mst.R		compute_mst.R
copy_inputs_flywheel.sh		copy_inputs_flywheel.sh
job_launcher.sh		job_launcher.sh
organize_inputs.sh		organize_inputs.sh
reslice_histo_segs.sh		reslice_histo_segs.sh
tau_density_to_atlas.sh		tau_density_to_atlas.sh
template_skel_analysis.sh		template_skel_analysis.sh