The code used for preparing the white matter masks and to perform tractography can be found in the script "tracto.py". The code used for bundles segmentation can be found in the script "afq.py", and "wmql.py" for the white matter query language. The script "density_maps.py" contains the code used for visualization of the results.
"afq.py" contains parts of the code of Automated Fiber Quantification [1] "My_forest.py" and "My_bagging.py" contains code of scikit-learn [2] that were adapted.
[1] Automated fiber quantification#. Automated Fiber Quantification - AFQ 0.12 documentation. (n.d.). Retrieved June 8, 2022, from https://yeatmanlab.github.io/pyAFQ/# [2] Scikit-Learn. (n.d.). Scikit-learn/scikit-learn at 37ac6788c9504ee409b75e5e24ff7d86c90c2ffb. GitHub. Retrieved June 8, 2022, from https://github.com/scikit-learn/scikit-learn/tree/37ac6788c9504ee409b75e5e24ff7d86c90c2ffb