About

This pipeline registers MRI to CT images for a patient (or a batch of patients) and applies the forward transforms from the registration to the ventilation images. --dir specifies either a single patient directory or a batch of patient directories.

Installing dependencies

Only install locally installed packages (excludes globally installed packages) and does not ask for user input

pip freeze --local --no-input > requirements.txt

Usage

If we have a directory called PIm_0123/, we can run the pipeline with:

git clone https://github.com/hbhutta/xe-mri.git
cd xe-mri
docker build --no-cache -t xe_mri_image .
docker run xe_mri_image --dir PIm_0123/

To get more information about flags, change the last command to:

docker run xe_mri_image --help