This project stores preprocessing and processing code for performing NODDI analysis (Zhang et al. 2011) at the PRL, URL, and LPZ in macular degeneration participants. Included are scripts setting up preprocessing using a basic FSL pipeline including topup and eddy. b0 images come from the diffusion scans themselves as opposed to SpinEcho fieldmaps. The NODDI toolbox used is version 1.01 that has been modified to remove status bar graphics and allow the pipeline to be run completely from the command line without needing the MATLAB GUI.
Scripts of interest are diff_preprocess.m that does basic file management and sets up the bash script to perform topup and eddy as well as noddi_MASTER that sets up the bash script to run NODDI.
Example preprocessing, NODDI processing, and registration scripts can be found in example-bash-scripts for one subject.
bet /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir98/unwarp_b0 /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir98/unwarp_b0_brain -m
bet /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir99/unwarp_b0 /data/user/mdefende/datasets/MDP-diff/subs/sub-MDP001/FSL/dir99/unwarp_b0_brain -m