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SurfNet: Reconstruction of Cortical Surfaces via Coupled Diffeomorphic Deformations

This is the repository for the paper.

Get started

conda env create -f environment.yaml

Model Training

For CNN-based SurfNet:

python3 surfNet_diff.py  --save_mesh_train True --hemisphere 'ths'   

For NODE-based SurfNet:

python surfNet_node.py --train_type='surf' --data_dir='/Documents/' --model_dir='./ckpts/experiment_1/model/' --data_name='adni'  --surf_hemi='lh' --surf_type='gm' --n_epochs=1000 --tag='exp1' --solver='euler' --step_size=0.1 --device='gpu'

Model Inference

For CNN-based SurfNet:

python3 eval_diff.py  --hemisphere 'lh'  

For NODE-based SurfNet:

python eval_node.py --test_type='eval'  --data_dir='/Documents/' --model_dir='./ckpts/experiment_1/model/' --result_dir='./ckpts/experiment_1/result/'  --data_name='adni' --surf_hemi='lh' --tag='exp1' --solver='euler' --step_size=0.1 --device='gpu'

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