This repository contains code for registration of FLAIR images and segmentation of white matter hyperintensity.
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First, download pipebuilder and pyniftitools. In your pipebuilder config file (
site.cfg
), specify the location where you downloadedpyniftitools
. -
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 alsoprocessed_0204
atlas_base
is the location of the atlas filesprocessed_0204
is currently a hardcoded version ofprocessing_root
, so if you changeprocessing_root
you should change this as well.site_average_path
is a location to save average maps for each site tovolume_csv_path
is a location to save CSV files with WMH volumes to
-
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.