Winniework/Automated-DTI-ALPS-pipeline ? reverse-engineered prompt

Build me a simple automated pipeline for DTI ALPS analysis from start to finish. I want one step to preprocess each subject’s diffusion data and another step to automatically calculate the left and right ALPS values from the processed files, then save everything into a results.csv file. It should also create a quick quality check image for each subject showing the ROI placement on the FA color map so I can review it fast.

Please make it work for multiple subjects in a folder, run each subject separately, and keep the process fully automatic with no manual ROI adjustment. If you need to look up current docs online for the imaging tools, go ahead. The end result should be easy to run from the command line, with clear inputs and outputs, and it should follow the same overall flow as a real DTI preprocessing and ALPS calculation workflow used in research.