stroke_processing - processing FLAIR images for stroke study

This repository contains code for registration of FLAIR images and segmentation of white matter hyperintensity.

Getting started

1. First, download pipebuilder and pyniftitools. In your pipebuilder config file (site.cfg), specify the location where you downloaded pyniftitools.

2. Set the appropriate paths in stroke.cfg.

   • site_subject_lists is a folder with per-site lists of all the subjects (site04.txt, site16.txt, etc).
   • processing_root is where you want to save the results to. See also processed_0204
   • atlas_base is the location of the atlas files
   • processed_0204 is currently a hardcoded version of processing_root, so if you change processing_root you should change this as well.
   • site_average_path is a location to save average maps for each site to
   • volume_csv_path is a location to save CSV files with WMH volumes to

3. Run the registration using scripts/process_stroke_site. For example, to process site 16:

    $ scripts/process_stroke_site.sh 16
   

   The pipeline code for this is located in stroke_processing/registration/flairpipe.py. Each Command has a short description of what it does.