This code here is designed to using fluid dynamic simulation to estimate the permeability of the vasculature structure.
There are 3 steps, and the reason is the simulation is very computationally heavy, thus the simulation part was designed to run on HPC with others parts can be finished on a workstation computer.
Step 1: Open RUN_THIS_FILE.m inside 001_Preparing folder in Matlab. Edit dir_root to locate your data folder. Run the file. The code will give you a .mat file named by your data folder.
Step 2: Move the .mat file from step 1 to desire HPC or workstation. Copy the content of 002_Voxel_CFD to the same folder. Edit the job_file_list to fit your file listing. Edit and run the RUN_THIS_FILE_slurm_batch (Each data will be submit to 20 node, so edit the job array accordingly). Each node will save the results as a .mat file.
Step 3: Download all the .mat files and put them in the 003_post_processing_1_collecting folder. Edit and run the RUN_THIS_FILE.m. This step will gives you a single integrated output as a .matfile.
- This module is designed to digest outcome of the STPT_vasculature_tracer.
Matlab 2019a elastix version 4.9.0
Free academic use.