Deriving new soft tissue contrasts from conventional MR images using deep learning

Versatile soft tissue contrast in magnetic resonance imaging is a unique advantage of the imaging modality. However, the versatility is not fully exploited. In this study, we propose a deep learning-based strategy to derive more soft tissue contrasts from conventional MR images obtained in standard clinical MRI. Two types of experiments are performed. First, MR images corresponding to different pulse sequences are predicted from one or more images already acquired. As an example, we predict T_1ρ weighted knee image from T₂ weighted image and/or T₁ weighted image. Furthermore, we estimate images corresponding to alternative imaging parameter values. In a representative case, variable flip angle images are predicted from a single T₁ weighted image, whose accuracy is further validated in quantitative T₁ map subsequently derived. To accomplish these tasks, images are retrospectively collected from 56 subjects, and self-attention convolutional neural network models are trained using 1104 knee images from 46 subjects and tested using 240 images from 10 other subjects. High accuracy has been achieved in resultant qualitative images as well as quantitative T₁ maps. The proposed deep learning method can be broadly applied to obtain more versatile soft tissue contrasts without additional scans or used to normalize MR data that were inconsistently acquired for quantitative analysis.     

Complementary use of T2-weighted and postcontrast T1- and T21-weighted imaging to distinguish sites of reversible and irreversible brain damage in focal ischemic lesions in the rat brain

The evolution of a photochemically induced cortical infarct was monitored using T₂-, postcontrast (GdDOTA) T₁-, and postcontrast (DyDTPA-BMA) T₂¹-weighted NMR imaging techniques. Data acquired with these different NMR imaging types were compared, both qualitatively and quantitatively. The T₂¹-weighted NMR images after sprodiamide injection (DyDTPA-BMA) were perfusion-weighted images that allowed the differentiation between several infarct-related areas in terms of different degrees of perfusion deficiency. No quantitative information on cerebral blood flow (CBF) was obtained. A clear distinction was made between areas with a complete lack of CBF located in the core of the lesion and temporary CBF insufficiencies in the rim surrounding this core. Concomitant observations on T₂-weighted and postcontrast T₁-weighted images revealed the same temporary rim characterized by an increased water content, and an intact blood-brain barrier (BBB), as well as by reduced perfusion. This rim appeared within the first hours after infarct induction, reached a maximum 24 h later, and lasted between 3–5 days, when its size gradually decreased until complete disappearance. These observations suggest the existence of an area at risk. Only on postcontrast T₁-weighted images, the core of the lesion remained visible during the whole experimental period (10 days) and reflected in all likelihood the irreversibly damaged ischemic central core. The combined application of different NMR imaging techniques when studying focal cerebral infarctions in the rat brain allowed us to distinguish, in terms of NMR characteristics, zones of reversible from irreversible brain damage and to estimate the severity of the damage. This might offer an appropriate experimental setup for the screening of cerebroprotective compounds.     

Relaxation-Time and Diffusion NMR Microscopy of Single Neurons

Relaxation-time and diffusion-weighted NMR micrographs have been obtained for single neurons isolated from Aplysia californica. These images allow the nucleus and cytoplasm to be clearly differentiated, in contrast to proton spin-density images, which appear relatively homogenous. Images of the spatial distribution of T₁ and T₂ relaxivities and the diffusion coefficient (D), as well as average values for T₁, T₂, and D in the cytoplasm and nucleus, were calculated from sets of appropriately weighted images. In all cases, water in the nucleus had relaxation and diffusion properties markedly differing from those of cytoplasmic water, which in turn had properties which were distinct from those of free water. Additionally, the cytoplasmic T₂ was observed to triple following cell death, which is attributed to cytoplasmic dilution as water enters the cell. The work presented represents the first effort at a consistent exploration of the spatial distribution of NMR characteristics of water within intact single cells. These studies have implications both for modeling the NMR characteristics of water in neuronal tissues based on an understanding of the characteristics of water in different cell compartments and for understanding water/macromolecule interactions within cells. NMR microscopy studies such as these may help form a foundation for understanding and interpreting NMR characteristics measured from large assemblies of cells, i.e., spectroscopy and imaging of living tissues.     

Study of γ-irradiation crosslinking ofcis-1,4-polybutadiene by NMR microscopy

Crosslink properties of ψ-irradiatedcis-1,4-polybutadiene (PB) were studied by NMR microscopy. Spin density images of the irradiated bulk materials show that crosslinking at the ?CH= atom dominates and the segments between two crosslinks are still flexible enough to twist, forming a dense material.T ₁ andT ₂ weighted images of these bulk materials show that theT ₁/T ₂ ratio increases upon irradiation. This is an indication of the increase of stiffness upon irradiation.¹H spin density images of the irradiated PB swollen in C₆D₆ show that the dimension of the cavities formed by irradiation is greater than the space resolution of the experiment.     

Molecular Diffusion in NMR Microscopy

The signal-to-noise ratio and the T₂ contrast in ¹H NMR microscopy are strongly affected by self-diffusion effects. Here, we investigate the free diffusion of water within imaging gradients. As a result we obtain an apparent relaxation time T₂ which in NMR microscopy is at least one order of magnitude smaller than the true T₂ value of water in the object. This apparent T₂ relaxation is considerably reduced by improving spatial resolution. We conclude that quantitative true T₂ values cannot be calculated from series of images with increasing echo time. Furthermore, from the knowledge of the apparent T₂, an optimum short echo time can be found in order to maximize signal-to-noise ratio. Our theoretical findings are confirmed by phantom experiments at 11.75 T field strength.     

Accelerating quantitative MR imaging with the incorporation of B1 compensation using deep learning

Quantitative magnetic resonance imaging (MRI) attracts attention due to its support to quantitative image analysis and data driven medicine. However, the application of quantitative MRI is severely limited by the long data acquisition time required by repetitive image acquisition and measurement of field map. Inspired by recent development of artificial intelligence, we propose a deep learning strategy to accelerate the acquisition of quantitative MRI, where every quantitative T₁ map is derived from two highly undersampled variable-contrast images with radiofrequency field inhomogeneity automatically compensated. In a multi-step framework, variable-contrast images are first jointly reconstructed from incoherently undersampled images using convolutional neural networks; then T₁ map and B₁ map are predicted from reconstructed images employing deep learning. Thus, the acceleration includes undersampling in every input image, a reduction in the number of variable contrast images, as well as a waiver of B₁ map measurement. The strategy is validated in T₁ mapping of cartilage. Acquired with a consistent imaging protocol, 1224 image sets from 51 subjects are used for the training of the prediction models, and 288 image sets from 12 subjects are used for testing. High degree of acceleration is achieved with image fidelity well maintained. The proposed method can be broadly applied to quantify other tissue properties (e.g. T₂, T_1ρ) as well.     

Quantitative NMR microscopy on intact plants

Quantitative high resolution images on intact young maize plants were acquired by using magnetization-prepared NMR microscopy. Although the spatial resolution is low compared with that of light microscopy, the calculated spin density and T₁ maps exhibit contrasts that are in excellent agreement with photomicrographic images. The T₂ map gives image contrasts that are not visible in a usual light microscopic image. The diffusion images show an anisotropic behavior of the water self-diffusion coefficient in the vascular bundles, which can be understood by the cell morphology in this plant section. This work demonstrates that quantitative imaging on intact plant systems is possible and that long total acquisition times are no obstacle. Furthermore, the different single parameter maps give a better insight into the morphology of plants under in vivo conditions.     

Magnetic,optical and relaxometric properties of organically coated gold–magnetite (Au–Fe3O4) hybrid nanoparticles for potential use in biomedical applications

We present the magnetic, optical and relaxometric properties of multifunctional Au–Fe₃O₄ hybrid nanoparticles (HNPs), as possible novel contrast agents (CAs) for magnetic resonance imaging (MRI). The HNPs have been synthesized by wet chemical methods in heterodimer and core–shell geometries and capped with oleylamine. Structural characterization of the samples have been made by X-ray diffraction and transmission electron microscopy, while magnetic properties have been investigated by means of Superconducting Quantum Interference Device-SQUID magnetometry experiments. As required for MRI applications using negative CAs, the samples resulted superparamagnetic at room temperature and well above their blocking temperatures. Optical properties have been investigated by analyzing the optical absorbtion spectra collected in UV–visible region. Relaxometric measurements have been performed on organic suspensions of HNPs and Nuclear Magnetic Resonance (NMR) dispersion curves have been obtained by measuring the longitudinal 1/T₁ and transverse 1/T₂ relaxation rates of solvent protons in the range 10 kHz/300 MHz at room temperature. NMR relaxivities r₁ and r₂ have been compared with ENDOREM^®, one of the commercial superparamagnetic iron oxide based MRI contrast agents. MRI contrast enhancement efficiencies have been investigated also by examining T₂-weighted MR images of suspensions. The experimental results suggest that the nanoparticles' suspensions are good candidates as negative CAs.     

Quantitative T2 Imaging of Plant Tissues By Means Of Multi-Echo MRI Microscopy

A method for quantitative T₂ imaging is presented which covers the large range of T₂ values in plants (5 to 2000 ms) simultaneously. The transverse relaxation is characterized by phase-sensitive measurement of many echo images in a multi-echo magnetic resonance imaging sequence. Up to 1000 signal-containing echo images can be measured with an inter-echo time of 2.5 ms at 0.47 T. Separate images of water density and of T₂ are obtained. Results on test samples, on the cherry tomato and on the stem of giant hogweed are presented. The effects of field strength, spatial resolution and echo time on the observed T₂ values is discussed. The combination of a relatively low magnetic field strength, short echo time and medium pixel resolution results in excellent T₂ contrast and in images hardly affected by susceptibility artifacts. The characterization of transverse relaxation by multi-echo image acquisition opens a new route for studies of water balance in plants.     

New pulse sequences for T1− and T1/T2−contrast enhancing in NMR imaging

Improved pulse sequences DIFN (abbreviation of the words: DIFferentiation by N pulses), 90° − τ₁ − 180° − τ₁ − … 180° − τ_n, with optimised time intervals τ₁ for T₁ measurement and contrast enhancing in NMR imaging are presented. The pulse sequences DIFN have a better sensitivity to T₁ than the well-known pulse sequence SR. In contrast to the IR pulse sequence, the information given by the DIFN pulse sequence is more reliable, because the NMR signal does not change its sign. For a given time interval τ₀ ≤ (0.1 − 0.3) T₁′ the DIFN pulse sequences serve as T₁-filters. They pass the signal components with relatively short T₁ < T₁′ and suppress the components with relatively long T₁ < T₁′. The effects of the radiofrequency field inhomogeneity and inaccurate adjusting of pulse lengths are also considered. It is also proposed in this work to use the joint T₁T₂-contrast in NMR imaging obtained as a result of applying the DIFN pulse sequences in combination with the well-known Carr-Purcell-Meiboom-Gill (CPMG) pulse sequence. The region of interest, where the contrast should be especially enhanced, is specified by the two times at which measurements are performed, which allow the amplitudes of pixels to reach some defined levels by spin-lattice and spin-spin relaxation.     

In vivo NMR imaging and T1 measurements of water protons in the human brain

Nuclear magnetic resonance (NMR) proton density images of the human brain have been made by the FONAR method. Spin-lattice relaxation times, T₁, of water hydrogen protons have been determined at random positions within frontal and temporal regions of the human brain. The primary purpose of this ongoing research is to accumulate a large data base of normal T₁ values for water protons in normal human brain tissue. Our experience to data includes 31 measurements on 18 volunteer subjects, and the mean value ± standard deviation is 215 ± 42 msec. In addition, two metastatic lesions of the brain were studied and found to have T₁ values longer than those for normal brain tissue.     

NMR imaging in human pregnancy: A preliminary study

In an effort to demonstrate the potential of nuclear magnetic resonance imaging (NMR) in the management of pregnancy, 15 patients in the first trimester and one in the third trimester of pregnancy have been investigated in the Aberdeen University NMR imager. Simple measurements of biparietal diameter and crown-rump length were made from both the NMR images and the ultrasound images on the same day, with good correlation between the two. The NMR data was displayed as inversion recovery, calculated T₁, proton density and S₁–S₂ images. The proton density and S₁–S₂ images were found to be the most useful for the demonstration of the fetus and for discriminating between placenta and uterus. The calculated T₁ data provided accurate quantification of the proton-spin lattice relaxation times of the different tissues, indicating that this measurement may be of use in the study of fetal brain development and placental function. The inversion recovery images showed poor tissue discrimination and were found to be of limited value. The unique information available using NMR and the non-invasive nature of the technique indicated that it should provide a useful method for the investigation of both fetal development and placental function in addition to making basic measurements of fetal size.     

Transverse relaxation time constraints on resolution in one-dimensional,phase- and frequency-encoded nuclear magnetic resonance imaging

The theoretical dependence of the resolution on the relationship of sampling time to transverse relaxation time (T₂) for frequency-encoded, one-dimensional NMR imaging using constant field gradients has been investigated. A resolution function that is explicitly dependent on the sampling time is derived, and it is shown that the observed image of an object can be written as a convolution of the sample magnetization with this resolution function. This function is explicitly calculated for two cases of interest: (1) for sampling times much shorter than T₂, and (2) for sampling times much longer than T₂. These cases are illustrated for two examples: (1) a uniform magnetic bar, and (2) uniform periodic magnetic bars. When oscillating gradients are utilized, these results still hold in the limit of slow oscillation. The resolution in phase-encoded NMR imaging is not explicitly dependent on the sampling time.     

Cerebral ischemic injury model of rat demonstrated withT 2-weighted magnetic resonance imaging

A photochemical reaction model of focal cerebral ischemic injury of rat was demonstrated by means of enhancedT ₂-weighted magnetic resonance imaging. The cerebral ischemia model was made using vein injection of rose bengal and irradiation by a beam of a cw laser with the wave-length of 514 nm. The ischemic injury region in rat brain can be found clearly in theT ₂-weighted magnetic resonance images in one hour, this time was calculated from the beginning of the laser irradiation to the end of the NMR data acquisition. It suggests thatT ₂-weighted imaging can find cerebral ischemia earlier than several hours after the onset of ischemia given in other papers. It also confirms that theT ₂-weighted magnetic resonance imaging approach should be of great potential to be applied in studying the cerebral ischemia.     

Solvent aided NMR microscopy of γ-irradiatedcis 1,4-polybutadiene

Cross-linked structure of γ-irradiatedcis 1,4-polybutadiene (PBi) was studied by NMR microscopy with the aid of deuterated benzene. After PBi was swollen (PBiS) in C₆D₆, the¹H NMR linewidth of the polymer was reduced from 4 to 2 kHz. The images show that the relaxation times,T ₁ andT ₂, of PBiS are longer than those of PBi. The simultaneous increase ofT ₁ andT ₂ implies that the molecular chains of PBi become more mobile upon swelling. The enhanced mobility of the molecular chains may provide a possibility of the increase in space resolution.     

Mössbauer study of the time evolution of the biochemical composition of the hematomas. Relationship with magnetic resonance imaging (MRI)

Biochemical constitution of the hematoma is depending of its evolution. In order to obtain a reliable diagnostic of the NMR images in case of vascular accidents, a systematic study of the time-evolution of hematomas has been performed, using Mössbauer spectrometry and complementary technics (ESR and visible absorption spectrophotometry). The change, in the course of time, of HbO₂ in deoxyhemoglobin Hb and other denaturation products (MHb, hemi- and hemochromes,…) are well-recognized on the different spectra.T ₁ andT ₂ NMR relaxation times are measured in the same time and their shortening is related to the appearance of the paramagnetic denaturation blood compounds.     

High field NMR microscopic imaging of cultivated strawberry fruit

The experimental conditions required for discrimination of various types of tissue in fruits of cultivated strawberry (Fragaria × Ananassa) at high fields (ca. 7 T) have been investigated. In marked contrast to soft fruits of other species, from which informative images have been derived at high fields using a variety of pulse sequences and acquisition parameters, appreciable image intensities from parenchymal and vascular tissues in healthy strawberry fruits were obtained only with a spin-echo imaging sequence using large sweep widths (ca. 100,000 Hz), and consequently small values for TE (<5 ms), indicating predominantly short T₂ values for these tissues. Damage caused by infection by the fungal pathogen Botrytis cinerea is readily seen as a result of a large increase in T₂ in the infected tissue, whereas ripening processes appear to be characterized primarily by small variations in the T₂-weighted contrast and in the relative magnitudes of T₁ between vascular and parenchymal tissue. In addition, it was possible selectively to enhance the contributions to images from the achenes (“seeds”) by using very short relaxation delays, thereby enhancing T₁-dominated contrast mechanisms.     

Basic concepts for nuclear magnetic resonance imaging

The basic concepts necessary to understand the physical basis of NMR imaging are presented in this didactic article. It is intended as a starting point for the radiologist or medical physicist who is addressing the topic of NMR for the first time. The basis of the NMR phenomena is described with introduction of the concepts of magnetic moment, magnetic fields, magnetic resonance, net magnetic moment of a sample, NMR excitation and NMR emission. The equipment necessary to observe these NMR properties of matter is summarized as well as the procedures for basic pulsed NMR experiments. The physical concepts for spatial localization of NMR emissions are introduced with physical analogies to stringed musical instruments. Several alternative imaging modalities are compared with greatest emphasis on the inversion recovery technique which yields images weighted by tissue T₁ values. The six subsystems of an NMR imaging device (primary magnet, computer, radio equipment, magnetic gradient, data storage and display subsystems) are described in an overview fashion. The paper is followed by a series of study questions to test the reader's comprehension of basic NMR imaging concepts.     

Prospective tissue-mimicking materials for use in NMR imaging phantoms

Water-based proteinaceous gels, which—with appropriate additives—are stable with time and possess a high melting point, have been used as base materials in ultrasonically tissue-mimicking materials. In the present work, versions of these gels having various concentrations of glycerol and graphite particles were studied regarding their NMR T₁ and T₂ dependencies at a proton Larmor frequency of 10.7 MHz. It has been found that T₁ depends primarily on the concentration of glycerol and T₂ depends primarily on the graphite particle concentration. Also, the ranges of T₁ and T₂ likely span those which exist for soft tissue parenchymae. Thus, these materials are good candidates for use as NMR tissue-mimicking materials. T₁ and T₂ also vary with gelatin concentration. The latter fact, together with the strong dependence of T₂ on graphite concentration, mean that effective contrast-resolution phantoms and anthropomorphic phantoms with stable T₁ and T₂ distributions can be produced.     

Quantification of cerebral perfusion using the "bookend technique": an evaluation in CNS tumors

We present a method of quantifying cerebral blood volume using dynamic susceptibility contrast. Our approach combines T₂-weighted echo planar imaging (EPI) pulse sequences and reference scans that determine the parenchymal T₁ changes resulting from an injection of a gadolinium chelate. This combined T₂- and T₁-weighted approach (the “bookend” technique) has been shown to be effective in the quantification of gradient-echo (GRE) (T₂*-weighted) perfusion images but has not been applied to spin-echo EPI (SE-EPI) (T₂-weighted) images. The physics related to blood volume measurement based on T₂- and T₂*-weighted EPI sequences is known to be different, and there is a question as to whether the bookend approach is effective with SE-EPI. We have compared the quantitative SE-EPI with GRE-EPI in a series of patients with central nervous system (CNS) tumors. We found that quantitative cerebral blood volume (qCBV) values for SE-EPI and GRE-EPI are in agreement with each other and with historical reference values. A subjective evaluation of image quality showed that image quality in the SE-EPI scans was high and exhibited high interreader agreement. We conclude that measuring qCBV using the bookend technique with SE-EPI images is possible and may be a viable alternative to GRE-EPI in the evaluation of CNS tumors.