Statistical estimation of T1 relaxation times using conventional magnetic resonance imaging

Whole Brain 3D T1 Mapping in Multiple Sclerosis Using Standard Clinical Images Compared to MP2RAGE and MR Fingerprinting

Quantitative T1 and T2 mapping is a useful tool to assess properties of healthy and diseased tissues. However, clinical diagnostic imaging remains dominated by relaxation-weighted imaging without direct collection of relaxation maps. Dedicated research sequences such as MR fingerprinting can save time and improve resolution over classical gold standard quantitative MRI (qMRI) methods, although they are not widely adopted in clinical studies. We investigate the use of clinical sequences in conjunction with prior knowledge provided by machine learning to elucidate T1 maps of brain in routine imaging studies without the need for specialized sequences. A classification learner was trained on T1w (magnetization prepared rapid gradient echo [MPRAGE]) and T2w (fluid-attenuated inversion recovery [FLAIR]) data (2.6 million voxels) from multiple sclerosis (MS) patients at 3T, compared to gold standard inversion recovery fast spin echo T1 maps in five healthy subjects, and tested on eight MS patients. In the MS patient test, the results of the machine learner-produced T1 maps were compared to MP2RAGE and MR fingerprinting T1 maps in seven tissue regions of the brain: cortical grey matter, white matter, cerebrospinal fluid, caudate, putamen and globus pallidus. Additionally, T1s in lesion-segmented tissue was compared using the three different methods. The machine learner (ML) method had excellent agreement with MP2RAGE, with all average tissue deviations less than 3.2%, with T1 lesion variation of 0.1%-5.3% across the eight patients. The machine learning method provides a valuable and accurate estimation of T1 values in the human brain while using data from standard clinical sequences and allowing retrospective reconstruction from past studies without the need for new quantitative techniques.

Field-cycling imaging yields repeatable brain R1 dispersion measurement at fields strengths below 0.2 Tesla with optimal fitting routine

OBJECTIVES

By rapidly changing magnetic field strength between 0.2 and 200 mT during the pulse sequence Field-Cycling Imaging (FCI) makes it possible to identify and evaluate new quantitative markers of pathology derived from dispersion of spin-lattice relaxation rate (R1) in vivo. The aim of this work was to determine the most effective approach to reliably estimate multi-field R1 dispersion measurements in brain tissue using FCI.

MATERIALS AND METHODS

This repeatability study consisted of twenty participants with moderate or severe small vessel disease. Each participant underwent 3 T MRI and FCI scans, repeated 30 days apart. After R1 maps were generated at 0.2, 2, 20, and 200 mT, co-registered tissue labels generated from 3 T MRI were used to extract tissue averaged values of R1 dispersion from regions of white matter (WM) and WM hyperintensities (WMHs).

RESULTS

The fitted model which yielded best overall image contrast between WM and WMH regions and R1 dispersion model adherence was determined. Tissue averaged values of R1 (0.2 mT) and R1 dispersion slope exhibited Cohen's d effect sizes of 3.07 and 1.48, respectively, between regions of WM and WMH. The cohort study results were repeatable between study visits.

DISCUSSION

Differences in R1 measurements could repeatably be discerned between normal and abnormal appearing brain tissues.

Improving magnetic resonance spectroscopy in the brainstem periaqueductal gray using spectral registration

PURPOSE

Functional understanding of the periaqueductal gray (PAG), a clinically relevant brainstem region, can be advanced using 1 H-MRS. However, the PAG's small size and high levels of physiological noise are methodologically challenging. This study aimed to (1) improve 1 H-MRS quality in the PAG using spectral registration for frequency and phase error correction; (2) investigate whether spectral registration is particularly useful in cases of greater head motion; and (3) examine metabolite quantification using literature-based or individual-based water relaxation times.

METHODS

Spectra were acquired in 33 healthy volunteers (50.1 years, SD = 17.19, 18 females) on a 3 T Philipps MR system using a point-resolved spectroscopy (PRESS) sequence optimized with very selective saturation pulses (OVERPRESS) and voxel-based flip angle calibration (effective volume of interest size: 8.8 × 10.2 × 12.2 mm3 ). Spectra were fitted using LCModel and SNR, NAA peak linewidths and Cramér-Rao lower bounds (CRLBs) were measured after spectral registration and after minimal frequency alignment.

RESULTS

Spectral registration improved SNR by 5% (p = 0.026, median value post-correction: 18.0) and spectral linewidth by 23% (p < 0.001, 4.3 Hz), and reduced the metabolites' CRLBs by 1% to 15% (p < 0.026). Correlational analyses revealed smaller SNR improvements with greater head motion (p = 0.010) recorded using a markerless motion tracking system. Higher metabolite concentrations were detected using individual-based compared to literature-based water relaxation times (p < 0.001).

CONCLUSION

This study demonstrates high-quality 1 H-MRS acquisition in the PAG using spectral registration. This shows promise for future 1 H-MRS studies in the PAG and possibly other clinically relevant brain regions with similar methodological challenges.

Experimental design and sample size considerations in longitudinal magnetic resonance imaging-based biomarker detection for multiple sclerosis

Several modeling approaches have been developed to quantify differences in multiple sclerosis lesion evolution on magnetic resonance imaging to identify the effect of treatment on disease progression. These studies have limited clinical applicability due to onerous scan frequency and lengthy study duration. Efficient methods are needed to reduce the required sample size, study duration, and sampling frequency in longitudinal magnetic resonance imaging studies. We develop a data-driven approach to identify parameters of study design for evaluation of longitudinal magnetic resonance imaging biomarkers of multiple sclerosis lesion evolution. Our design strategies are considerably shorter than those described in previous studies, thus having the potential to lower costs of clinical trials. From a dataset of 36 multiple sclerosis patients with at least six monthly magnetic resonance imagings, we extracted new lesions and performed principal component analysis to estimate a biomarker that recapitulated lesion recovery. We tested the effect of multiple sclerosis disease modifying therapy on the lesion evolution index in three experimental designs and calculated sample sizes needed to appropriately power studies. Our proposed methods can be used to calculate required sample size and scan frequency in observational studies of multiple sclerosis disease progression as well as in designing clinical trials to find effects of treatment on multiple sclerosis lesion evolution.

A Spatio-Temporal Model for Longitudinal Image-on-Image Regression

Neurologists and radiologists often use magnetic resonance imaging (MRI) in the management of subjects with multiple sclerosis (MS) because it is sensitive to inflammatory and demyelinative changes in the white matter of the brain and spinal cord. Two conventional modalities used for identifying lesions are T1-weighted (T1) and T2-weighted fluid-attenuated inversion recovery (FLAIR) imaging, which are used clinically and in research studies. Magnetization transfer ratio (MTR), which is available only in research settings, is an advanced MRI modality that has been used extensively for measuring disease-related demyelination both in white matter lesions as well across normal-appearing white matter. Acquiring MTR is not standard in clinical practice, due to the increased scan time and cost. Hence, prediction of MTR based on the modalities T1 and FLAIR could have great impact on the availability of these promising measures for improved patient management. We propose a spatio-temporal regression model for image response and image predictors that are acquired longitudinally, with images being co-registered within the subject but not across subjects. The model is additive, with the response at a voxel being dependent on the available covariates not only through the current voxel but also on the imaging information from the voxels within a neighboring spatial region as well as their temporal gradients. We propose a dynamic Bayesian estimation procedure that updates the parameters of the subject-specific regression model as data accummulates. To bypass the computational challenges associated with a Bayesian approach for high-dimensional imaging data, we propose an approximate Bayesian inference technique. We assess the model fitting and the prediction performance using longitudinally acquired MRI images from 46 MS patients.

MIMoSA: An Automated Method for Intermodal Segmentation Analysis of Multiple Sclerosis Brain Lesions

BACKGROUND AND PURPOSE

Magnetic resonance imaging (MRI) is crucial for in vivo detection and characterization of white matter lesions (WMLs) in multiple sclerosis. While WMLs have been studied for over two decades using MRI, automated segmentation remains challenging. Although the majority of statistical techniques for the automated segmentation of WMLs are based on single imaging modalities, recent advances have used multimodal techniques for identifying WMLs. Complementary modalities emphasize different tissue properties, which help identify interrelated features of lesions.

METHODS

Method for Inter-Modal Segmentation Analysis (MIMoSA), a fully automatic lesion segmentation algorithm that utilizes novel covariance features from intermodal coupling regression in addition to mean structure to model the probability lesion is contained in each voxel, is proposed. MIMoSA was validated by comparison with both expert manual and other automated segmentation methods in two datasets. The first included 98 subjects imaged at Johns Hopkins Hospital in which bootstrap cross-validation was used to compare the performance of MIMoSA against OASIS and LesionTOADS, two popular automatic segmentation approaches. For a secondary validation, a publicly available data from a segmentation challenge were used for performance benchmarking.

RESULTS

In the Johns Hopkins study, MIMoSA yielded average Sørensen-Dice coefficient (DSC) of .57 and partial AUC of .68 calculated with false positive rates up to 1%. This was superior to performance using OASIS and LesionTOADS. The proposed method also performed competitively in the segmentation challenge dataset.

CONCLUSION

MIMoSA resulted in statistically significant improvements in lesion segmentation performance compared with LesionTOADS and OASIS, and performed competitively in an additional validation study.

Joint Intensity Fusion Image Synthesis Applied to Multiple Sclerosis Lesion Segmentation

We propose a new approach to Multiple Sclerosis lesion segmentation that utilizes synthesized images. A new method of image synthesis is considered: joint intensity fusion (JIF). JIF synthesizes an image from a library of deformably registered and intensity normalized atlases. Each location in the synthesized image is a weighted average of the registered atlases; atlas weights vary spatially. The weights are determined using the joint label fusion (JLF) framework. The primary methodological contribution is the application of JLF to MRI signal directly rather than labels. Synthesized images are then used as additional features in a lesion segmentation task using the OASIS classifier, a logistic regression model on intensities from multiple modalities. The addition of JIF synthesized images improved the Dice-Sorensen coefficient (relative to manually drawn gold standards) of lesion segmentations over the standard model segmentations by 0.0462 ± 0.0050 (mean ± standard deviation) at optimal threshold over all subjects and 10 separate training/testing folds.

A LAG FUNCTIONAL LINEAR MODEL FOR PREDICTION OF MAGNETIZATION TRANSFER RATIO IN MULTIPLE SCLEROSIS LESIONS

We propose a lag functional linear model to predict a response using multiple functional predictors observed at discrete grids with noise. Two procedures are proposed to estimate the regression parameter functions: (1) an approach that ensures smoothness for each value of time using generalized cross-validation; and (2) a global smoothing approach using a restricted maximum likelihood framework. Numerical studies are presented to analyze predictive accuracy in many realistic scenarios. The methods are employed to estimate a magnetic resonance imaging (MRI)-based measure of tissue damage (the magnetization transfer ratio, or MTR) in multiple sclerosis (MS) lesions, a disease that causes damage to the myelin sheaths around axons in the central nervous system. Our method of estimation of MTR within lesions is useful retrospectively in research applications where MTR was not acquired, as well as in clinical practice settings where acquiring MTR is not currently part of the standard of care. The model facilitates the use of commonly acquired imaging modalities to estimate MTR within lesions, and outperforms cross-sectional models that do not account for temporal patterns of lesion development and repair.

Statistical estimation of white matter microstructure from conventional MRI

Diffusion tensor imaging (DTI) has become the predominant modality for studying white matter integrity in multiple sclerosis (MS) and other neurological disorders. Unfortunately, the use of DTI-based biomarkers in large multi-center studies is hindered by systematic biases that confound the study of disease-related changes. Furthermore, the site-to-site variability in multi-center studies is significantly higher for DTI than that for conventional MRI-based markers. In our study, we apply the Quantitative MR Estimation Employing Normalization (QuEEN) model to estimate the four DTI measures: MD, FA, RD, and AD. QuEEN uses a voxel-wise generalized additive regression model to relate the normalized intensities of one or more conventional MRI modalities to a quantitative modality, such as DTI. We assess the accuracy of the models by comparing the prediction error of estimated DTI images to the scan-rescan error in subjects with two sets of scans. Across the four DTI measures, the performance of the models is not consistent: Both MD and RD estimations appear to be quite accurate, while AD estimation is less accurate than MD and RD; the accuracy of FA estimation is poor. Thus, in some cases when assessing white matter integrity, it may be sufficient to acquire conventional MRI sequences alone.

PREVAIL: Predicting Recovery through Estimation and Visualization of Active and Incident Lesions

Objective

The goal of this study was to develop a model that integrates imaging and clinical information observed at lesion incidence for predicting the recovery of white matter lesions in multiple sclerosis (MS) patients.

Methods

Demographic, clinical, and magnetic resonance imaging (MRI) data were obtained from 60 subjects with MS as part of a natural history study at the National Institute of Neurological Disorders and Stroke. A total of 401 lesions met the inclusion criteria and were used in the study. Imaging features were extracted from the intensity-normalized T₁-weighted (T₁w) and T₂-weighted sequences as well as magnetization transfer ratio (MTR) sequence acquired at lesion incidence. T₁w and MTR signatures were also extracted from images acquired one-year post-incidence. Imaging features were integrated with clinical and demographic data observed at lesion incidence to create statistical prediction models for long-term damage within the lesion.

Validation

The performance of the T₁w and MTR predictions was assessed in two ways: first, the predictive accuracy was measured quantitatively using leave-one-lesion-out cross-validated (CV) mean-squared predictive error. Then, to assess the prediction performance from the perspective of expert clinicians, three board-certified MS clinicians were asked to individually score how similar the CV model-predicted one-year appearance was to the true one-year appearance for a random sample of 100 lesions.

Results

The cross-validated root-mean-square predictive error was 0.95 for normalized T₁w and 0.064 for MTR, compared to the estimated measurement errors of 0.48 and 0.078 respectively. The three expert raters agreed that T₁w and MTR predictions closely resembled the true one-year follow-up appearance of the lesions in both degree and pattern of recovery within lesions.

Conclusion

This study demonstrates that by using only information from a single visit at incidence, we can predict how a new lesion will recover using relatively simple statistical techniques. The potential to visualize the likely course of recovery has implications for clinical decision-making, as well as trial enrichment.

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A model for predicting degree and pattern of MS lesion tissue recovery is proposed.

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The model relies solely on MR images at lesion incidence and patient information.

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Predictions performed well when rated for accuracy by expert MS clinicians.