Multi-delay arterial spin-labeled perfusion estimation with biophysics simulation and deep learning

Purpose: To develop biophysics-based method for estimating perfusion Q from arterial spin labeling (ASL) images using deep learning. Methods: A 3D U-Net (QTMnet) was trained to estimate perfusion from 4D tracer propagation images. The network was trained and tested on simulated 4D tracer concentration data based on artificial vasculature structure generated by constrained constructive optimization (CCO) method. The trained network was further tested in a synthetic brain ASL image based on vasculature network extracted from magnetic resonance (MR) angiography. The estimations from both trained network and a conventional kinetic model were compared in ASL images acquired from eight healthy volunteers. Results: QTMnet accurately reconstructed perfusion Q from concentration data. Relative error of the synthetic brain ASL image was 7.04% for perfusion Q, lower than the error using single-delay ASL model: 25.15% for Q, and multi-delay ASL model: 12.62% for perfusion Q. Conclusion: QTMnet provides accurate estimation on perfusion parameters and is a promising approach as a clinical ASL MRI image processing pipeline.

Physics-based network fine-tuning for robust quantitative susceptibility mapping from high-pass filtered phase

Purpose: To improve the generalization ability of convolutional neural network (CNN) based prediction of quantitative susceptibility mapping (QSM) from high-pass filtered phase (HPFP) image. Methods: The proposed network addresses two common generalization issues that arise when using a pre-trained network to predict QSM from HPFP: a) data with unseen voxel sizes, and b) data with unknown high-pass filter parameters. A network fine-tuning step based on a high-pass filtering dipole convolution forward model is proposed to reduce the generalization error of the pre-trained network. A progressive Unet architecture is proposed to improve prediction accuracy without increasing fine-tuning computational cost. Results: In retrospective studies using RMSE, PSNR, SSIM and HFEN as quality metrics, the performance of both Unet and progressive Unet was improved after physics-based fine-tuning at all voxel sizes and most high-pass filtering cutoff frequencies tested in the experiment. Progressive Unet slightly outperformed Unet both before and after fine-tuning. In a prospective study, image sharpness was improved after physics-based fine-tuning for both Unet and progressive Unet. Compared to Unet, progressive Unet had better agreement of regional susceptibility values with reference QSM. Conclusion: The proposed method shows improved robustness compared to the pre-trained network without fine-tuning when the test dataset deviates from training. Our code is available at https://github.com/Jinwei1209/SWI_to_QSM/

Maximum Spherical Mean Value (mSMV) Filtering for Whole Brain Quantitative Susceptibility Mapping

To develop a tissue field filtering algorithm, called maximum Spherical Mean Value (mSMV), for reducing shadow artifacts in quantitative susceptibility mapping (QSM) of the brain without requiring brain tissue erosion. Residual background field is a major source of shadow artifacts in QSM. The mSMV algorithm filters large field values near the border, where the maximum value of the harmonic background field is located. The effectiveness of mSMV for artifact removal was evaluated by comparing with existing QSM algorithms in a simulated numerical brain, 11 healthy volunteers, by assessing image quality in routine clinical patient study $(n=43)$, and by measuring lesion susceptibility values in multiple sclerosis patients $(n=50)$, a total of $n=93$ patients. Numerical simulation showed that mSMV reduces shadow artifacts and improves QSM accuracy. Better shadow reduction, as demonstrated by lower QSM variation in the gray matter and higher QSM image quality score, was also observed in healthy subjects and in patients with hemorrhages, stroke and multiple sclerosis. The mSMV algorithm allows reconstruction of QSMs that are equivalent to those obtained using SMV-filtered dipole inversion without eroding the volume of interest.

mcLARO: Multi-Contrast Learned Acquisition and Reconstruction Optimization for simultaneous quantitative multi-parametric mapping

Purpose: To develop a method for rapid sub-millimeter T1, T2, T2* and QSM mapping in a single scan using multi-contrast Learned Acquisition and Reconstruction Optimization (mcLARO). Methods: A pulse sequence was developed by interleaving inversion recovery and T2 magnetization preparations and single-echo and multi-echo gradient echo acquisitions, which sensitized k-space data to T1, T2, T2* and magnetic susceptibility. The proposed mcLARO used a deep learning framework to optimize both the multi-contrast k-space under-sampling pattern and the image reconstruction based on image feature fusion. The proposed mcLARO method with R=8 under-sampling was validated in a retrospective ablation study using fully sampled data as reference and evaluated in a prospective study using separately acquired conventionally sampled quantitative maps as reference standard. Results: The retrospective ablation study showed improved image sharpness of mcLARO compared to the baseline network without multi-contrast sampling pattern optimization or image feature fusion, and negligible bias and narrow 95% limits of agreement on regional T1, T2, T2* and QSM values were obtained by the under-sampled reconstructions compared to the fully sampled reconstruction. The prospective study showed small or negligible bias and narrow 95% limits of agreement on regional T1, T2, T2* and QSM values by mcLARO (5:39 mins) compared to reference scans (40:03 mins in total). Conclusion: mcLARO enabled fast sub-millimeter T1, T2, T2* and QSM mapping in a single scan.

LARO: Learned Acquisition and Reconstruction Optimization to accelerate Quantitative Susceptibility Mapping

Quantitative susceptibility mapping (QSM) involves acquisition and reconstruction of a series of images at multi-echo time points to estimate tissue field, which prolongs scan time and requires specific reconstruction technique. In this paper, we present our new framework, called Learned Acquisition and Reconstruction Optimization (LARO), which aims to accelerate the multi-echo gradient echo (mGRE) pulse sequence for QSM. Our approach involves optimizing a Cartesian multi-echo k-space sampling pattern with a deep reconstruction network. Next, this optimized sampling pattern was implemented in an mGRE sequence using Cartesian fan-beam k-space segmenting and ordering for prospective scans. Furthermore, we propose to insert a recurrent temporal feature fusion module into the reconstruction network to capture signal redundancies along echo time. Our ablation studies show that both the optimized sampling pattern and proposed reconstruction strategy help improve the quality of the multi-echo image reconstructions. Generalization experiments show that LARO is robust on the test data with new pathologies and different sequence parameters. Our code is available at https://github.com/Jinwei1209/LARO.git.

Motion Artifact Reduction in Quantitative Susceptibility Mapping using Deep Neural Network

An approach to reduce motion artifacts in Quantitative Susceptibility Mapping using deep learning is proposed. We use an affine motion model with randomly created motion profiles to simulate motion-corrupted QSM images. The simulated QSM image is paired with its motion-free reference to train a neural network using supervised learning. The trained network is tested on unseen simulated motion-corrupted QSM images, in healthy volunteers and in Parkinson's disease patients. The results show that motion artifacts, such as ringing and ghosting, were successfully suppressed.

Temporal Feature Fusion with Sampling Pattern Optimization for Multi-echo Gradient Echo Acquisition and Image Reconstruction

Quantitative imaging in MRI usually involves acquisition and reconstruction of a series of images at multi-echo time points, which possibly requires more scan time and specific reconstruction technique compared to conventional qualitative imaging. In this work, we focus on optimizing the acquisition and reconstruction process of multi-echo gradient echo pulse sequence for quantitative susceptibility mapping as one important quantitative imaging method in MRI. A multi-echo sampling pattern optimization block extended from LOUPE-ST is proposed to optimize the k-space sampling patterns along echoes. Besides, a recurrent temporal feature fusion block is proposed and inserted into a backbone deep ADMM network to capture the signal evolution along echo time during reconstruction. Experiments show that both blocks help improve multi-echo image reconstruction performance.

NeRD: Neural Representation of Distribution for Medical Image Segmentation

We introduce Neural Representation of Distribution (NeRD) technique, a module for convolutional neural networks (CNNs) that can estimate the feature distribution by optimizing an underlying function mapping image coordinates to the feature distribution. Using NeRD, we propose an end-to-end deep learning model for medical image segmentation that can compensate the negative impact of feature distribution shifting issue caused by commonly used network operations such as padding and pooling. An implicit function is used to represent the parameter space of the feature distribution by querying the image coordinate. With NeRD, the impact of issues such as over-segmenting and missing have been reduced, and experimental results on the challenging white matter lesion segmentation and left atrial segmentation verify the effectiveness of the proposed method. The code is available via https://github.com/tinymilky/NeRD.

DEEPMIR: A DEEP convolutional neural network for differential detection of cerebral Microbleeds and IRon deposits in MRI

Background: Cerebral microbleeds (CMBs) and non-hemorrhage iron deposits in the basal ganglia have been associated with brain aging, vascular disease and neurodegenerative disorders. Recent advances using quantitative susceptibility mapping (QSM) make it possible to differentiate iron content from mineralization in-vivo using magnetic resonance imaging (MRI). However, automated detection of such lesions is still challenging, making quantification in large cohort bases studies rather limited. Purpose: Development of a fully automated method using deep learning for detecting CMBs and basal ganglia iron deposits using multimodal MRI. Materials and Methods: We included a convenience sample of 24 participants from the MESA cohort and used T2-weighted images, susceptibility weighted imaging (SWI), and QSM to segment the lesions. We developed a protocol for simultaneous manual annotation of CMBs and non-hemorrhage iron deposits in the basal ganglia, which resulted in defining the gold standard. This gold standard was then used to train a deep convolution neural network (CNN) model. Specifically, we adapted the U-Net model with a higher number of resolution layers to be able to detect small lesions such as CMBs from standard resolution MRI which are used in cohort-based studies. The detection performance was then evaluated using the cross-validation principle in order to ensure generalization of the results. Results: With multi-class CNN models, we achieved an average sensitivity and precision of about 0.8 and 0.6, respectively for detecting CMBs. The same framework detected non-hemorrhage iron deposits reaching an average sensitivity and precision of about 0.8. Conclusions: Our results showed that deep learning could automate the detection of small vessel disease lesions and including multimodal MR data such as QSM can improve the detection of CMB and non-hemorrhage iron deposits.

Geometric Loss for Deep Multiple Sclerosis lesion Segmentation

Multiple sclerosis (MS) lesions occupy a small fraction of the brain volume, and are heterogeneous with regards to shape, size and locations, which poses a great challenge for training deep learning based segmentation models. We proposed a new geometric loss formula to address the data imbalance and exploit the geometric property of MS lesions. We showed that traditional region-based and boundary-aware loss functions can be associated with the formula. We further develop and instantiate two loss functions containing first- and second-order geometric information of lesion regions to enforce regularization on optimizing deep segmentation models. Experimental results on two MS lesion datasets with different scales, acquisition protocols and resolutions demonstrated the superiority of our proposed methods compared to other state-of-the-art methods.