Dynamic CBCT imaging using prior model-free spatiotemporal implicit neural representation (PMF-STINR).

OBJECTIVE: Dynamic cone-beam computed tomography (CBCT) can capture high-spatial-resolution, time-varying images for motion monitoring, patient setup, and adaptive planning of radiotherapy. However, dynamic CBCT reconstruction is an extremely ill-posed spatiotemporal inverse problem, as each CBCT volume in the dynamic sequence is only captured by one or a few X-ray projections, due to the slow gantry rotation speed and the fast anatomical motion (e.g., breathing). Approach: We developed a machine learning-based technique, prior-model-free spatiotemporal implicit neural representation (PMF-STINR), to reconstruct dynamic CBCTs from sequentially acquired X-ray projections. PMF-STINR employs a joint image reconstruction and registration approach to address the under-sampling challenge, enabling dynamic CBCT reconstruction from singular X-ray projections. Specifically, PMF-STINR uses spatial implicit neural representations to reconstruct a reference CBCT volume, and it applies temporal INR to represent the intra-scan dynamic motion with respect to the reference CBCT to yield dynamic CBCTs. PMF-STINR couples the temporal INR with a learning-based B-spline motion model to capture time-varying deformable motion during the reconstruction. Compared with the previous methods, the spatial INR, the temporal INR, and the B-spline model of PMF-STINR are all learned on the fly during reconstruction in a one-shot fashion, without using any patient-specific prior knowledge or motion sorting/binning. Main results: PMF-STINR was evaluated via digital phantom simulations, physical phantom measurements, and a multi-institutional patient dataset featuring various imaging protocols (half-fan/full-fan, full sampling/sparse sampling, different energy and mAs settings, etc.). The results showed that the one-shot learning-based PMF-STINR can accurately and robustly reconstruct dynamic CBCTs and capture highly irregular motion with high temporal (~0.1s) resolution and sub-millimeter accuracy. Significance: PMF-STINR can reconstruct dynamic CBCTs and solve the intra-scan motion problem from conventional 3D CBCT scans without using any prior anatomical/motion model or motion sorting/binning. It can be a promising tool for motion management by offering richer motion information than traditional 4D-CBCTs.

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 anatomical dynamics. However, the reconstruction of 3D cine-MRI is challenged by highly under-sampled 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 under-sampled 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 that 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. 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 two MR datasets acquired clinically from human subjects. Its reconstruction accuracy was also compared with that of the model-based non-rigid motion estimation method (MR-MOTUS) and a deep learning-based method (TEMPEST).Main results. STINR-MR can reconstruct 3D cine-MR images with high temporal (<100 ms) and spatial (3 mm) resolutions. Compared with MR-MOTUS and TEMPEST, 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 ± SD center-of-mass error of 0.9 ± 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.

Dynamic CBCT Imaging using Prior Model-Free Spatiotemporal Implicit Neural Representation (PMF-STINR).

Objective: Dynamic cone-beam computed tomography (CBCT) can capture high-spatial-resolution, time-varying images for motion monitoring, patient setup, and adaptive planning of radiotherapy. However, dynamic CBCT reconstruction is an extremely ill-posed spatiotemporal inverse problem, as each CBCT volume in the dynamic sequence is only captured by one or a few X-ray projections, due to the slow gantry rotation speed and the fast anatomical motion (e.g., breathing). Approach: We developed a machine learning-based technique, prior-model-free spatiotemporal implicit neural representation (PMF-STINR), to reconstruct dynamic CBCTs from sequentially acquired X-ray projections. PMF-STINR employs a joint image reconstruction and registration approach to address the under-sampling challenge, enabling dynamic CBCT reconstruction from singular X-ray projections. Specifically, PMF-STINR uses spatial implicit neural representation to reconstruct a reference CBCT volume, and it applies temporal INR to represent the intra-scan dynamic motion with respect to the reference CBCT to yield dynamic CBCTs. PMF-STINR couples the temporal INR with a learning-based B-spline motion model to capture time-varying deformable motion during the reconstruction. Compared with the previous methods, the spatial INR, the temporal INR, and the B-spline model of PMF-STINR are all learned on the fly during reconstruction in a one-shot fashion, without using any patient-specific prior knowledge or motion sorting/binning. Main results: PMF-STINR was evaluated via digital phantom simulations, physical phantom measurements, and a multi-institutional patient dataset featuring various imaging protocols (half-fan/full-fan, full sampling/sparse sampling, different energy and mAs settings, etc.). The results showed that the one-shot learning-based PMF-STINR can accurately and robustly reconstruct dynamic CBCTs and capture highly irregular motion with high temporal (~0.1s) resolution and sub-millimeter accuracy. Significance: PMF-STINR can reconstruct dynamic CBCTs and solve the intra-scan motion from conventional 3D CBCT scans without using any prior anatomical/motion model or motion sorting/binning. It can be a promising tool for motion management by offering richer motion information than traditional 4D-CBCTs.

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.

Dynamic cone-beam CT reconstruction using spatial and temporal implicit neural representation learning (STINR).

Objective. Dynamic cone-beam CT (CBCT) imaging is highly desired in image-guided radiation therapy to provide volumetric images with high spatial and temporal resolutions to enable applications including tumor motion tracking/prediction and intra-delivery dose calculation/accumulation. However, dynamic CBCT reconstruction is a substantially challenging spatiotemporal inverse problem, due to the extremely limited projection sample available for each CBCT reconstruction (one projection for one CBCT volume).Approach. We developed a simultaneous spatial and temporal implicit neural representation (STINR) method for dynamic CBCT reconstruction. STINR mapped the unknown image and the evolution of its motion into spatial and temporal multi-layer perceptrons (MLPs), and iteratively optimized the neuron weightings of the MLPs via acquired projections to represent the dynamic CBCT series. In addition to the MLPs, we also introduced prior knowledge, in the form of principal component analysis (PCA)-based patient-specific motion models, to reduce the complexity of the temporal mapping to address the ill-conditioned dynamic CBCT reconstruction problem. We used the extended-cardiac-torso (XCAT) phantom and a patient 4D-CBCT dataset to simulate different lung motion scenarios to evaluate STINR. The scenarios contain motion variations including motion baseline shifts, motion amplitude/frequency variations, and motion non-periodicity. The XCAT scenarios also contain inter-scan anatomical variations including tumor shrinkage and tumor position change.Main results. STINR shows consistently higher image reconstruction and motion tracking accuracy than a traditional PCA-based method and a polynomial-fitting-based neural representation method. STINR tracks the lung target to an average center-of-mass error of 1-2 mm, with corresponding relative errors of reconstructed dynamic CBCTs around 10%.Significance. STINR offers a general framework allowing accurate dynamic CBCT reconstruction for image-guided radiotherapy. It is a one-shot learning method that does not rely on pre-training and is not susceptible to generalizability issues. It also allows natural super-resolution. It can be readily applied to other imaging modalities as well.