tsantini/wmh_seg repository overview

This is a containerized version of the code from https://github.com/jinghangli98/wmh_seg⁠

If you use this, please cite:

Li, J., Santini, T., Huang, Y., Mettenburg, J. M., Ibrahim, T. S., Aizenstein, H. J., & Wu, M. (2024). wmh_seg: Transformer based U-Net for Robust and Automatic White Matter Hyperintensity Segmentation across 1.5 T, 3T and 7T. arXiv preprint arXiv:2402.12701. https://arxiv.org/abs/2402.12701⁠

Usage example:

docker run -v "$PWD":"$PWD" -w "$PWD" -it tsantini/wmh_seg
wmh_seg -i FLAIR.nii.gz -o WMH_segmentation.nii.gz
or
for files in *FLAIR.nii.gz; do wmh_seg -i $files -o wmh_seg_$files -v -b 4; done