WMmorphology

code for white matter morphology project

Steps for studying white matter morphology

Preprocess diffusion files
run AFQ and Dan's fibers
Using the output from AFQ, run script to create volumes from each fiber group - need to get from Dan
run script to create surfaces from each volume - createsurfallfibers.m
run sript to get shapeDNA of each surface file - get_shapeDNA
read .ev (shapeDNA) files into python - parse_ev_files.py
do some ML on the data

Preprocessing steps for HCP data

download the subjects from HCP
the T1 is already ACPC aligned, just going to use that for now, otherwise do ACPC alignment
split the diffusion data into separate shells, going to use shell 2000 for now run batch_split.m
do Dti init