Instruction

train.py is the training script.

Dataset: Several brain MRI datasets are publicly available online: IXI, ADNI, OASIS, ABIDE, etc. Note that those datasets may not contain labels (segmentation). To generate labels, you can use FreeSurfer, which is an open-source software for normalizing brain MRI images. Here are some useful commands in FreeSurfer: Brain MRI preprocessing and subcortical segmentation using FreeSurfer.

Reference:

TransUnet

ViT-pytorch

VoxelMorph