MR to CT Registration

This was developed to properly register CT to MR images, and to fix issues with LeGui with bad-registrations and flipped MR images.

It contains two main entry points. One to fix legui, another to run a MR to CT registration

Building

You only need to do this once!

Cluster, no Python 3.9 available

This requires Python 3.9 or later. To run this on the cluster, where this is not available, it's easiest to

1. build a singularity image that contains Python 3.10
2. Run that image with exec, with file path bindings back to this source code to set up a python environment
3. Run that image with exec, with the above binddings to this source code, and to /data/ to process data

To build the image:

1. cd to the top directory of this solution
2. In bash: build-as-apptainer/build-python-only.sh

With Python 3.9 or later available

Build the environment (once only)

/.build.sh

Running

Register MR to CT

Cluster, no Python 3.9 available

./RegisterMRToCT.sh --t1 path-to-your-t1.nii --ct path-to-your-ct.nii --out path-to-a-directory-to-save-to

With Python 3.9 or 3.10 available

# Activate once per session
env/bin/activate

# Run with Python
env/bin/python3.10 -m RegisterMRToCT

Fix Legui

Check main.sh and main.py for details

Cluster, no Python 3.9 available

Not implemented.

With Python 3.9 available

./main.sh /directory/containing/legui/folder /path/to/t1

will output to /directory/containing/legui/fixed_legui/