Conditional Temporal Attention Networks for Neonatal Cortical Surface Reconstruction

This is the official PyTorch implementation of the paper: Conditional Temporal Attention Networks for Neonatal Cortical Surface Reconstruction (MICCAI 2023).

Installation

The Conditional Temporal Attention Network (CoTAN) requires the following dependencies:

• PyTorch == 1.7.1
• PyTorch3D == 0.4.0 (for training only)
• Pandas == 1.2.4 (for training only)
• Nibabel == 3.2.1
• NumPy == 1.23.4
• ANTsPy == 0.3.4 (for registration only)
• SciPy == 1.10.0 (for registration only)

Dataset

We use the third release of the dHCP neonatal dataset (download). Once downloaded, the brain-extracted T2-weighted MRI images should be affinely aligned to the MNI-152 space. A clipped and brain-extracted MNI-152 template is provided in ./template/mni152_brain_clip.nii.gz. We use ANTsPy for affine registration, and please run

python register.py --move_path='/MOVE_PATH/moving_img.nii.gz'\
                   --save_path='/SAVE_PATH/warped_img.nii.gz'

to align the moving_img to the MNI template. The aligned/warped image will be saved to /SAVE_PATH/warped_img.nii.gz. After registration, we assume that the dataset has the following file structure:

/YOUR_DATASET
    /train
        /sub-CC00050XX01_ses-7201
            /sub-CC00050XX01_ses-7201_T2w_brain_affine.nii.gz
            /sub-CC00050XX01_ses-7201_left_white.surf.gii
            /sub-CC00050XX01_ses-7201_left_pial.surf.gii
            /sub-CC00050XX01_ses-7201_right_white.surf.gii
            /sub-CC00050XX01_ses-7201_right_pial.surf.gii
        /sub-CC00051XX02_ses-7702
            /...
        /...
    /valid
        /...
    /test
        /...
    /combined.csv

where *_T2w_brain_affine.nii.gz is the affinely aligned T2w images, and combined.csv is the metadata (download) containing the scan age of the subjects.

Training

To train CoTAN for left (right) white (pial) surface reconstruction, please run:

python train.py --data_path='/YOUR_DATASET/'\
                --model_path='./model/'\
                --surf_type='white'\
                --surf_hemi='left'\
                --data_name='dhcp'\
                --tag='EXP_ID'\
                --step_size=0.02\
                --n_epoch=200\
                --device='cuda:0'

where data_path is the directory of your dataset, model_path is the directory to save the log and checkpoints of training, surf_type=['wm','pial'] is the type of the surface, surf_hemi==['left','right'] is the brain hemisphere, data_name is a string to identify your dataset, tag is a string to identify your experiments, step_size is the step size for integration, and n_epoch is the number of epochs for training. For the details of all arguments please run python train.py --help.

Evaluation

For the inference, please run:

python pred.py --data_path='/YOUR_DATASET/YOUR_T2_MRI.nii.gz'\
               --save_path='/YOUR_RESULT/'\
               --age=40.0

where data_path is the file name of your affinely aligned T2w brain MRI, and age is the scan age (week) of your subject. The predicted surfaces will be saved to your save_path in GIfTI format .surf.gii. For visualization of the surfaces, we recommend to use Connectome Workbench, which visualizes the predicted cortical surfaces as follows.