pytransformix

A python3 wrapper for transformix, a command-line utility provided as part of the package elastix

Currently runs on MacOS and Linux.

Installation

Step 1

Either pip install from PyPI:

pip install transformix

or first git clone the repo and then pip install from your clone:

cd ~/repos  # Or wherever on your computer you want to download this code to
git clone https://github.com/jasper-tms/pytransformix.git
cd pytransformix
pip install .

Step 2

Install elastix by first downloading it from the releases page. Operating system compatibility notes:

• Ubuntu 22.04: Use elastix-5.1.0 or the latest version.
• Ubuntu 20.04: Use elastix-5.0.1
• Ubuntu 18.04: Use elastix-5.0.0
• Ubuntu 16.04: Use elastix-4.9.0
• MacOS: elastix-5.0.1 worked on Big Sur, and I haven't tested other combinations. Probably safe to download the latest version.

Then extract the .zip or .tar.gz file you downloaded and put the folder somewhere on your computer. Then add that folder's bin subdirectory to your shell PATH and that folder's lib subdirectory to your shell LD_LIBRARY_PATH. For example, if you put the folder at ~/software/elastix-5.0.1-linux, then add these three lines of text

export PATH=$HOME/software/elastix-5.0.1-linux/bin:$PATH
export LD_LIBRARY_PATH=$HOME/software/elastix-5.0.1-linux/lib${LD_LIBRARY_PATH+:$LD_LIBRARY_PATH}
export DYLD_LIBRARY_PATH=$HOME/software/elastix-5.0.1-linux/lib${DYLD_LIBRARY_PATH+:$DYLD_LIBRARY_PATH}

to your shell config file (~/.bashrc for bash on Linux, ~/.bash_profile for bash on Mac, or ~/.zshrc for zsh on Mac). Then open up a new terminal and run elastix. If you see Use "elastix --help" for information about elastix-usage., you're good to go. If not, feel free to open an issue and I can try to help.