This assumes you have the correct data in the folder. Everything can be run from the .ipynb file provided.
If you would like to get the data, please do the following
''' !wget wget http://surfer.nmr.mgh.harvard.edu/ftp/data/neurite/data/neurite-oasis.2d.v1.0.tar -O data.tar !tar -xf data.tar; '''
Or download from the following link: https://github.com/adalca/medical-datasets/blob/master/neurite-oasis.md
If you would like to load the pretrained weights, make sure you set 'load_weights' in TemplateCreation to True, and ensure that the path to the vxmDense model you'd like to load is correct.
To train a General Registration Network, follow the below command
cd Project5/voxelmorph/scripts/torch/register_train.py
python train.py --img-list train_list.txt --model-dir . --bidir
Model checkpoints can be found within project5/voxelmorph/models/
All the instructions and results can be found within Project5/project5.ipynb