This is the official repo for the CVPR 2024 paper "Fully Convolutional Slice-to-Volume Reconstruction (FC-SVR) for Single-Stack MRI" by Sean I Young, Yaël Balbastre, Bruce Fischl and others. See https://arxiv.org/abs/2312.03102.
All pre-requisite python packages are listed in pytorch_1.13.1.yml. Run conda env create -f pytorch_1.13.1.yml.
Also, FreeSurfer version 7 is required to prepare the training dataset. See https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads
The Havard CRL fetal atlases can be downloaded from http://crl.med.harvard.edu/research/fetal_brain_atlas. Preprocess the data using preprocess/crl.py
The FeTA training and validation volumes can be downloaded from https://doi.org/10.7303/syn25649159. Preprocess the data using preprocess/feta.py
Run feta3d_svr_train.sh to train the svr model on the FeTA 2.1 data. Run feta3d_inpaint_train.sh to train the interpolation model.
The pretrained weights for motion estimation and interpolation networks will be posted here soon! In the mean time, I can send them to you if you email me at siyoung at mit dot edu
Feel free to reach out to me via e-mail and say hello if you have interesting ideas for extensions, applications or if you simply just want to chat!