This segmentation toolbox is designed for 3D Brain MRI volume segmentation. It divides 3D MRI volume into several patches and perform multi-label segmentation. The labels for the overlapping region of patches are determined by calculating the average probability map.

To train the model, set the training data directory in train.py and run the file. The weights of the trained model will be save to the models/ folder

Measures a dice scores between the prediction and ground truth. Run test.py

Dr.Adrian Dalca's voxelmoprh https://github.com/voxelmorph/voxelmorph

Unsupervised Learning for Fast Probabilistic Diffeomorphic Registration Adrian V. Dalca, Guha Balakrishnan, John Guttag, Mert R. Sabuncu MICCAI 2018. eprint arXiv:1805.04605

An Unsupervised Learning Model for Deformable Medical Image Registration Guha Balakrishnan, Amy Zhao, Mert R. Sabuncu, John Guttag, Adrian V. Dalca CVPR 2018. eprint arXiv:1802.02604

For and problems or questions, please send me an email at [email protected]