Scripts for building a 3D atlas of tau burden from MRI and histology

Data organization

For each subject/specimen, the following data are required:

input/[id]/mold_mri/mtl7t.nii.gz

this is the 7T MRI scan
input/[id]/mold_mri/contour_image.nii.gz

this is the level set segmentation of the scan (ITK-SNAP) -4 on the inside, +4 on the outside, 0 at the boundary
input/[id]/mold_mri/slitmold.nii.gz

this is the image of the 3D printed mold.
input/[id]/mold_mri/holderrotation.mat

this is the rotation of the MRI into the mold space

Name		Name	Last commit message	Last commit date
Latest commit History 78 Commits
bids_src		bids_src
docs		docs
histo-burden		histo-burden
histo-preproc		histo-preproc
itksnap		itksnap
yaml		yaml
.gitignore		.gitignore
README.md		README.md
ashs_grid.sh		ashs_grid.sh
bf_rand_samp.sh		bf_rand_samp.sh
blockface_z_match.R		blockface_z_match.R
common.sh		common.sh
copy_input.sh		copy_input.sh
copy_sadhanas_segs.sh		copy_sadhanas_segs.sh
curve_metric.py		curve_metric.py
fit_multichannel.R		fit_multichannel.R
hot_colormap.txt		hot_colormap.txt
import_svs.sh		import_svs.sh
integrate_density_over_samples.py		integrate_density_over_samples.py
lb_bf_mri_reg.json		lb_bf_mri_reg.json
lb_ihc_nissl_reg.json		lb_ihc_nissl_reg.json
lb_mold_to_hires_reg.json		lb_mold_to_hires_reg.json
lb_nissl_mri_reg.json		lb_nissl_mri_reg.json
lightbox.sh		lightbox.sh
list_gs.sh		list_gs.sh
man_seg_itksnap.txt		man_seg_itksnap.txt
metric_stats.sh		metric_stats.sh
process_raw_slide.py		process_raw_slide.py
pybatch.sh		pybatch.sh
rebase_cmd.sh		rebase_cmd.sh
recon.sh		recon.sh
reg_eval_labels.txt		reg_eval_labels.txt
runme.sh		runme.sh
stage_x16.sh		stage_x16.sh
svs_to_cloud.sh		svs_to_cloud.sh