3D cine-magnetic resonance imaging using spatial and temporal implicit neural representation learning (STINR-MR)

OBJECTIVE: 3D cine-magnetic resonance imaging (cine-MRI) can capture images of the human body volume with high spatial and temporal resolutions to study the anatomical dynamics. However, the reconstruction of 3D cine-MRI is challenged by highly undersampled k-space data in each dynamic (cine) frame, due to the slow speed of MR signal acquisition. We proposed a machine learning-based framework, spatial and temporal implicit neural representation learning (STINR-MR), for accurate 3D cine-MRI reconstruction from highly undersampled data. APPROACH: STINR-MR used a joint reconstruction and deformable registration approach to achieve a high acceleration factor for cine volumetric imaging. It addressed the ill-posed spatiotemporal reconstruction problem by solving a reference-frame 3D MR image and a corresponding motion model which deforms the reference frame to each cine frame. The reference-frame 3D MR image was reconstructed as a spatial implicit neural representation (INR) network, which learns the mapping from input 3D spatial coordinates to corresponding MR values. The dynamic motion model was constructed via a temporal INR, as well as basis deformation vector fields (DVFs) extracted from prior/onboard 4D-MRIs using principal component analysis (PCA). The learned temporal INR encodes input time points and outputs corresponding weighting factors to combine the basis DVFs into time-resolved motion fields that represent cine-frame-specific dynamics. STINR-MR was evaluated using MR data simulated from the 4D extended cardiac-torso (XCAT) digital phantom, as well as MR data acquired clinically from a healthy human subject. Its reconstruction accuracy was also compared with that of the model-based non-rigid motion estimation method (MR-MOTUS). MAIN RESULTS: STINR-MR can reconstruct 3D cine-MR images with high temporal (<100 ms) and spatial (3 mm) resolutions. Compared with MR-MOTUS, STINR-MR consistently reconstructed images with better image quality and fewer artifacts and achieved superior tumor localization accuracy via the solved dynamic DVFs. For the XCAT study, STINR reconstructed the tumors to a mean±S.D. center-of-mass error of 1.0±0.4 mm, compared to 3.4±1.0 mm of the MR-MOTUS method. The high-frame-rate reconstruction capability of STINR-MR allows different irregular motion patterns to be accurately captured. SIGNIFICANCE: STINR-MR provides a lightweight and efficient framework for accurate 3D cine-MRI reconstruction. It is a ‘one-shot’ method that does not require external data for pre-training, allowing it to avoid generalizability issues typically encountered in deep learning-based methods.