Optimization of MRI protocols and pulse sequence parameters for eigenimage filtering

The objective of the study was to examine the utility of double inversion recovery (DIR) magnetic resonance imaging (MRI) using a 3-T magnetic resonance imager in the preoperative evaluation of hippocampal sclerosis (HS) in patients with mesial temporal lobe epilepsy. This retrospective study had institutional review board approval, and informed consent was obtained. Twelve patients with unilateral HS and 12 age-matched healthy control subjects were included. Imaging was performed using DIR, fluid-attenuated inversion recovery (FLAIR), and T2-weighted turbo spin-echo (T2 TSE) sequences vertical to the hippocampal axis. Quantitative assessment for hippocampus of the patients and control subjects was determined. Regions of interest (ROIs) were placed on bilateral hippocampi, and signal intensity was measured. The signal-to-noise ratio (SNR) of ipsilateral hippocampus, contrast ratio of ipsilateral-to-contralateral side, contrast-to-noise ratio (CNR), and asymmetry index of bilateral hippocampi were calculated and compared among the 3 sequences. Statistical analyses were performed with 1-way analysis of variance and Student t test. On DIR images, HS demonstrated extremely high signal intensity. The hippocampi ipsilateral to the seizure focus showed significantly increased signal intensity, as compared with contralateral hippocampi and healthy subjects (F = 47.876, P < 0.001). The higher SNR of ipsilateral hippocampus on DIR was significant compared with the FLAIR and T2 TSE (P < 0.01). The CNR of bilateral hippocampi on DIR was also significantly higher than that on the FLAIR and T2 TSE (P < 0.01). However, compared with the FLAIR, no significant differences of contrast ratio and asymmetry index between bilateral hippocampi were observed on DIR. Double inversion recovery brain imaging reveals characteristically extremely high signal intensity of hippocampus in patients with HS. Double inversion recovery images can describe HS with high SNR and CNR superior to conventional magnetic resonance sequences and can be valuable for the diagnosis of HS.

Chapter 2 - Pulse Sequences for Diffusion-weighted MRI

ObjectiveTo identify the optimal pulse sequence for ferumoxides-enhanced magnetic resonance (MR) imaging in the detection of hepatocelluar carcinomas (HCCs).Materials and MethodsSixteen patients with 25 HCCs underwent MR imaging following intravenous infusion of ferumoxides. All MR studies were performed on a 1.5-T MR system, using a phased-array coil. Ferumoxides (Feridex IV) at a dose of 15 µmol/Kg was slowly infused intravenously, and axial images of seven sequences were obtained 30 minutes after the end of infusion. The MR protocol included fast spin-echo (FSE) with two echo times (TR3333 8571/TE18 and 90-117), singleshot FSE (SSFSE) with two echo times (TR∞/TE39 and 98), T2*-weighted gradient-recalled acquisition in the steady state (GRASS) (TR216/TE20), T2*-weighted fast multiplanar GRASS (FMPGR) (TR130/TE8.4-9.5), and T2*-weighted fast multiplanar spoiled GRASS (FMPSPGR) (TR130/TE8.4-9.5). Contrast-to-noise ratios (CNRs) of HCCs determined during the imaging sequences formed the basis of quantitative analysis, and images were qualitatively assessed in terms of lesion conspicuity and image artifacts. The diagnostic accuracy of all sequences was assessed using receiver operating characteristic (ROC) analysis.ResultsQuantitative analysis revealed that the CNRs of T2*-weighted FMPGR and T2*-weighted FMPSPGR were significantly higher than those of the other sequences, while qualitative analysis showed that image artifacts were prominent at T2*-weighted GRASS imaging. Lesion conspicuity was statistically significantly less clear at SSFSE imaging. In term of lesion detection, T2*-weighted FMPGR, T2*-weighted FMPSPGR, and proton density FSE imaging were statistically superior to the others.ConclusionT2*-weighted FMPGR, T2*-weighted FMPSPGR, and proton density FSE appear to be the optimal pulse sequences for ferumoxides-enhanced MR imaging in the detection of HCCs.

Continued improvements in diagnostic accuracy using magnetic resonance (MR) imaging will require development of methods for tissue analysis that complement traditional qualitative MR imaging studies. Quantitative MR imaging is based on measurement and interpretation of tissue-specific parameters independent of experimental design, compared with qualitative MR imaging, which relies on interpretation of tissue contrast that results from experimental pulse sequence parameters. Quantitative MR imaging represents a natural next step in the evolution of MR imaging practice, since quantitative MR imaging data can be acquired using currently available qualitative imaging pulse sequences without modifications to imaging equipment. The article presents a review of the basic physical concepts used in MR imaging and how quantitative MR imaging is distinct from qualitative MR imaging. Subsequently, the article reviews the hierarchical organization of major applicable pulse sequences used in this article, with the sequences organized into conventional, hybrid, and multispectral sequences capable of calculating the main tissue parameters of T1, T2, and proton density. While this new concept offers the potential for improved diagnostic accuracy and workflow, awareness of this extension to qualitative imaging is generally low. This article reviews the basic physical concepts in MR imaging, describes commonly measured tissue parameters in quantitative MR imaging, and presents the major available pulse sequences used for quantitative MR imaging, with a focus on the hierarchical organization of these sequences. ©RSNA, 2017.

Many treatment options are available to patients with endometrial, cervical, or ovarian cancer. Magnetic resonance (MR) imaging plays an important role in the patient journey from the initial evaluation of the extent of the disease to appropriate treatment selection and follow-up. The purpose of this review is to highlight the added role of MR imaging in the treatment stratification and overall care of patients with endometrial, cervical, or ovarian cancer. Several MR imaging techniques used in evaluation of patients with gynecologic malignancies are described, including both anatomic MR imaging sequences (T1- and T2-weighted sequences) and pulse sequences that characterize tissue on the basis of physiologic features (diffusion-weighted MR imaging), dynamic contrast agent-enhanced MR imaging, and MR spectroscopy. MR imaging findings corresponding to the 2009 revised International Federation of Gynecology and Obstetrics staging of gynecologic malignancies are also described in detail, highlighting possible pearls and pitfalls of staging. With the growing role of the radiologist as a core member of the multidisciplinary treatment planning team, it is crucial for imagers to recognize that MR imaging has become central in tailoring treatment options and therapy in patients with gynecologic malignancies.

Context Brain Magnetic Resonance Imaging (MRI) involves multiple sequences and relatively long acquisition times. These factors can affect image quality and present challenges that necessitate continuous evaluation and optimisation to ensure diagnostic efficiency. Aim To assess the image quality and average acquisition time of adult brain MRI sequences on a 1.5T scanner. Methods This prospective study evaluated adult brain MRI images of consenting patients at a local MRI center in Nigeria.The assessment focused on the following axial sequences: T1-weighted (T1W) T2-weighted (T2W) Fluid Attenuation Inversion Recovery (FLAIR) Image Quality Evaluation: Quantitative: Signal-to-noise ratio (SNR) Contrast-to-noise ratio (CNR) Qualitative: Visual Grading Analysis (VGA) performed by four observers with over 5 years of experience The acquisition time for each sequence was recorded. Data were analyzed using VGA and SPSS version 25. Results A total of 100 adult brain MRI examinations were analyzed. Quantitative Findings T1W demonstrated the highest SNR for: Grey matter: 51.58 White matter: 40.16 T2W produced the highest CNR: 9.23 FLAIR displayed the lowest SNR and CNR among the evaluated sequences. Qualitative Findings T2W achieved the highest VGA score: 4.75 FLAIR was rated lowest in qualitative image quality. Acquisition Time T1W had the longest scan time: 5 minutes 38 seconds T2W had the shortest acquisition time: 2 minutes 43 seconds Conclusion T2-weighted sequences demonstrated superior contrast-to-noise ratio and visual grading scores compared to T1W and FLAIR, suggesting better overall diagnostic image quality. While T1W achieved the highest SNR, its relatively long acquisition time highlights the need for optimisation. FLAIR performed poorest in both qualitative and quantitative parameters, indicating an area for potential protocol improvement.

Magnetic resonance imaging (MRI) is a research field of high interest as the implementation of new imaging modalities can significantly improve clinical diagnosis of several human pathologies. Awake nonhuman animals in the laboratory are being used in MRI pre-clinical systems for the validation of new imaging techniques, but animal welfare concerns emerge as MRI pulse sequences produce extremely loud sounds, up to 120 dB. Consequently, it is unclear how stressful these sounds are to the animals. Here, the impact of these sounds in the rodent behavior and physiology was evaluated. To achieve this, C57BL6/J mice were divided into two groups: a group exposed to sounds of typical pulse sequences used in imaging and a control group that was not exposed to those sounds. Mice have been tested in the open field and elevated plus maze to monitor baseline behavior and a hormonal stress biomarker was assayed to assess acute stress. The results indicate that the pulse sequences used in MRI are transient stressors that overall do not impact the behavioral status of the animals.

<h3>Objective:</h3> Magnetic resonance imaging (MRI) and clinical parameters are associated with disease progression in multiple sclerosis (MS). The aim of this study was to investigate whether adding MRI parameters to a model with only clinical parameters could improve these associations. <h3>Methods:</h3> 89 patients (55 women) with recently diagnosed MS had clinical and MRI evaluation at baseline (time of diagnosis) and at follow-up after 2.2 years. Detailed clinical data were available, including disease type (relapse-onset or progressive-onset) and disability, as measured by the Expanded Disability Status Scale (EDSS). MRI parameters included Normalised Brain Volume (NBV) at baseline, percentage brain volume change (PBVC/year), T2- and T1-lesion loads and spinal cord abnormalities. Progression of disability (increase in EDSS of at least 1 point at follow-up) was the main outcome measure. For a model containing only clinical parameters, the added value of MRI parameters was tested using logistic regression. <h3>Results:</h3> PBVC/year and lesion loads at follow-up were significantly higher in the group with progression. Adding PBVC/year to a clinical model improved the model, indicating that MRI parameters added independent information (p&lt;0.001). <h3>Conclusion:</h3> The rate of cerebral atrophy conveys added information for the progression of disability in patients with early MS, suggesting that clinical disability is determined by neurodegenerative changes as depicted by MRI.

To evaluated the impact of a deep learning (DL)-based image reconstruction on multi-arterial-phase magnetic resonance imaging (MA-MRI) for small hypervascular hepatic masses in patients who underwent gadoxetic acid-enhanced liver MRI. We retrospectively enrolled 55 adult patients (aged ≥ 18years) with small hepatic hypervascular mass (≤ 3cm) between December 2022 and February 2023. All patients underwent MA-MRI, subsequently reconstructed with a DL-based application. Qualitative assessment with Linkert scale including motion artifact (MA), liver edge (LE), hepatic vessel clarity (HVC) and image quality (IQ) was performed. Quantitative image analysis including signal to noise ratio (SNR), contrast to noise ratio (CNR) and noise was performed. On both arterial phases (APs), all qualitative parameters were significantly improved after DL-based image reconstruction. (LE on 1st AP, 1.22 vs 1.61; LE on 2nd AP, 1.21 vs 1.65; HVC on 1st AP, 1.24 vs 1.39; HVC on 2nd AP, 1.24 vs 1.44; IQ on 1st AP, 1.17 vs 1.45; IQ on 2nd AP, 1.17 vs 1.47, all p values < 0.05). The SNR, CNR and noise were significantly improved after DL-based image reconstruction. (SNR on AP1, 279.08 vs 176.14; SNR on AP2, 334.34 vs 199.24; CNR on AP1, 106.09 vs 64.14; CNR on AP2, 129.66 vs 73.73; noise on AP1, 1.51 vs 2.33; noise on AP2, 1.45 vs 2.28, all p values < 0.05). Gadoxetic acid-enhanced MA-MRI with DL-based image reconstruction improved the qualitative and quantitative parameters. Despite the short acquisition time, high-quality MA-MRI is now achievable.

Purpose: To optimize contrast to noise ratio (CNR) in magnetic resonance imaging (MRI) of prostate cancer using at 3T. Methods: CNR was expressed as a difference in MR signals of two samples. Amulti-echo spin-echo (MESE) pulse sequence was used. The theoretical value of the maximum CNR was obtained using the derivative of CNR with echo time (TE) as a variable. The T1 relaxation time was ignored as repetition time (TR) was assumed to be very long (TR >> T1). The theoretical calculations were confirmed with in vitro and in vivo experiments. For in vitro experiments we used samples with different T2 values using various concentrations of super paramagnetic iron oxide (SPIO) and for in vivo experiments we used an animal model of prostate cancer. Results: CNR was maximized by selecting the optimum TE for a multi-echo spin-echo (MESE) pulse sequence based on theoretical predictions. MR images of prostate cancer at 3T were obtained and showed maximum CNR at the predicted TE. Conclusions: It was possible to maximize CNR of prostate tumour by selecting the optimal TE based on simple theoretical calculations. The proposed method can be applied to other pulse sequences and tissues. It can be applied to any MRI system at any magnetic field. However the method requires knowledge of T2 relaxation times.

The group of Multiplied, Added, Subtracted and/or fiTted Inversion Recovery (MASTIR) pulse sequences in which usually two or more inversion recovery (IR) images of different types are combined is described, and uses for this type of sequence are outlined. IR sequences of different types can be multiplied, added, subtracted, and/or fitted together to produce variants of the MASTIR sequence. The sequences provide a range of options for increasing image contrast, demonstrating specific tissues and fluids of interest, and suppressing unwanted signals. A formalism using the concept of pulse sequences as tissue property filters is used to explain the signal, contrast and weighting of the pulse sequences with both univariate and multivariate filter models. Subtraction of one magnitude reconstructed IR image from another with a shorter TI can produce very high T1 dependent positive contrast from small increases in T1. The reverse subtracted IR sequence can provide high positive contrast enhancement with gadolinium chelates and iron deposition which decrease T1. Additional contrast to that arising from increases in T1 can be produced by supplementing this with contrast arising from concurrent increases in ρm and T2, as well as increases or decreases in diffusion using subtraction IR with echo subtraction and/or diffusion subtraction. Phase images may show 180º differences as a result of rotating into the transverse plane both positive and negative longitudinal magnetization. Phase images with contrast arising in this way, or other ways, can be multiplied by magnitude IR images to increase the contrast of the latter. Magnetization Transfer (MT) and susceptibility can be used with IR sequences to improve contrast. Selective images of white and brown adipose tissue lipid and water components can be produced using different TIs and in and out-of-phase TEs. Selective images of ultrashort and short T2 tissue components can be produced by nulling long T2 tissue components with an inversion pulse and subtraction of images with longer TEs from images with ultrashort TEs. The Double Echo Sliding IR (DESIRE) sequence provides images with a wide range of TIs from which it is possible to choose values of TI to achieve particular types of tissue and/or fluid contrast (e.g., for subtraction with different TIs, as described above, and for long T2 tissue signal nulling with UTE sequences). Unwanted tissue and fluid signals can be suppressed by addition and subtraction of phase-sensitive (ps) and magnitude reconstructed images. The sequence also offers options for synergistic use of the changes in blood and tissue ρm, T1, T2/T2*, D* and perfusion that can be seen with fMRI of the brain. In-vivo and ex-vivo illustrative examples of normal brain, cartilage, multiple sclerosis, Alzheimer's disease, and peripheral nerve imaged with different forms of the MASTIR sequence are included.

Contrast-Enhanced Magnetic Resonance Imaging (CE-MRI) has been widely used in the diagnosis of lesions. Many contrast agents with various chemical and pharmacokinetic properties have been developed for clinical use. The signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) after the contrast agent administration depend on many factors, e.g. category and injected dosage of contrast agents, field strength of magnetic resonance (MR) scanner, slew rate of gradient, type of radiofrequency coil, reconstruction algorithm, pulse sequences, and so on. Gadovist is a newly developed contrast agent with high formulation of 1.0 M. It has been used in MR angiography and perfusion studies. The aim of this study is to investigate the optimal concentrations of Gadovist in MR T1-weighted (T1W) images from phantom study and computer simulation. A phantom made of 21 test tubes with various concentrations of Gadovist (0–160 mM) was investigated. All the studies were performed on a 1.5-T clinical whole-body scanner. Four T1W pulse sequences, including two-dimensional spoiled gradient echo (2DSPGR), three-dimensional fast spoiled gradient echo (3DFSPGR), conventional spin echo (CSE), and inversion recovery (IR) were employed to produce T1W images. The CNR values were calculated from regions of interest (ROIs) of all test tubes and the optimal concentration for each pulse sequence was determined. The T1 and T2 values of the phantom were also measured to obtain the relaxivities (r1 and r2). Afterward, the optimal concentration for each pulse sequence could be obtained from computer simulation by using the r1 and r2 values. The results showed that the measured optimal concentrations for 2DSPGR, 3DFSPGR, CSE and IR are 10, 20, 2.5, and 2.5 mM, respectively. The r1 and r2 values of the Gadovist phantom are 4.1 and 5.7 mM-1s-1, respectively. The optimal concentrations obtained from computer simulation are 13.5, 22.8, 2.0, and 2.7 mM for 2DSPGR, 3DFSPGR, CSE, and IR, respectively. The optimal concentrations obtained from computer simulation and phantom study are in good agreement.

To evaluate the use of contrast material-enhanced magnetic resonance (MR) imaging with conventional T1-weighted gradient-recalled echo (GRE) and inversion-recovery (IR)-prepared GRE methods to quantitatively measure the size of irreversible electroporation (IRE) ablation zones in the liver in a rat model. All studies were approved by the institutional animal care and use committee and were performed in accordance with institutional guidelines. Seventeen adult male Sprague-Dawley rats were divided into four groups. Rats in groups 1-3 (n = 15 total) underwent IRE performed by using different IRE parameters after gadopentetate dimeglumine administration. Rats in group 4 (n = 2) underwent IRE ablation without prior gadopentetate dimeglumine injection to serve as control animals. MR imaging measurements (with conventional T1-weighted GRE and IR-prepared GRE methods) were performed 2 hours after IRE to predict the IRE ablation zones, which were correlated with pathology-confirmed necrosis areas 24 hours after IRE by using the Spearman correlation coefficient. Bland-Altman plots were also generated to investigate the agreement between MR imaging-measured ablation zones and reference standard histologic measurements of corresponding ablation zones. The necrotic areas measured on the pathology images were well correlated with the hyperintense regions measured on T1-weighted GRE images (r = 0.891, P < .001) and normal tissue-nulled IR images (r = 0.874, P < .001); pathology measurements were also well correlated with the smaller hyperintense regions measured on those IR images with inversion times specifically selected to null signal from the peripheral penumbra surrounding the ablation zone (r = 0.939, P < .001). Bland-Altman plots indicated that these penumbra-nulled IR images provided more accurate predictions of IRE ablation zones, with T1-weighted GRE measurements tending to overestimate ablation zone sizes. Contrast-enhanced MR imaging permits accurate depiction of ablated tissue zones after IRE procedures. IR-prepared contrast-enhanced MR imaging can be used to quantitatively measure IRE ablation zones in the liver. http://radiology.rsna.org/lookup/suppl/doi:10.1148/radiol.10100645/-/DC1.

Functional magnetic resonance imaging (fMRI) is a unique window to the brain, enabling scientists to follow changes in brain activity in response to hormones, ageing, environment, drugs of abuse and other stimuli. There are two features that make fMRI unique when compared with other imaging modalities used in behavioural neuroscience. First, it can be entirely noninvasive: each animal can serve as its own control over the natural course of its life, vital for following neuroadaptation and other developmental processes critical to understanding behaviour. Second, fMRI has the spatial and temporal resolution to observe patterns of neuronal activity across the entire brain in less than a minute. Although fMRI does not have the cellular spatial resolution of immunostaining, nor the millisecond temporal resolution of electrophysiology, synchronised changes in neuronal activity across multiple brain areas seen with functional MRI can be viewed as functional neuroanatomical circuits coordinating the thoughts, memories and emotions for particular behaviours. Thus, fMRI affords a systems approach to the study of the brain, complementing and building from other neurobiological techniques to understand how behaviour is organised across multiple brain regions. In this review, we present a general background to fMRI and the different imaging modalities that can be used in fMRI studies. Included are examples of the application of fMRI in behavioural neuroscience research, along with discussion of the advantages and disadvantages of this technology.

Ultrashort echo time (UTE) image to directly visualize short T2 tissues requires postprocessing for the suppression of the surrounding long T2 tissues in a clinical magnetic resonance imaging (MRI) scanner. Weighted subtraction of UTE images with an optimal weighting factor could provide high positive contrast with adequate suppression. To demonstrate in-vivo UTE MRI with weighted subtractions of dual echo UTE imaging using a 3 T clinical MRI and to determine the optimal weighting factors through the analyses of signal-to-noise ratios (SNRs) and contrast-to-noise ratios (CNRs). Forty-seven consecutive knee MR including dual echo 3D UTE sequence (TE of 70 µs and 3.82 ms) were reviewed. Seven patients with normal findings in the knee MR were included in the current study. For variably weighted subtraction images, the initial UTE image was rescaled relative to that of the second echo image with weighting factors from 0.1 to 4.0. Thirty-five pairs of the ROI measurements of the UTE image and second long echo images were repeated after 2 weeks. For quantitative assessment, SNR and CNR were measured from the ROIs on the patellar tendon, cartilage, cortical bone, meniscus, and infrapatellar fat pad. Intra-observer agreement was assessed by using both Cohen's Kappa and Bland-Altman approach. The short T2 tissue could be visualized with adequate suppression on the subtraction images. Considering the CNRs and SNRs, the optimal ranges of the weighting factors could be suggested: 0.3 for the tendon, 0.4 for the cortical bone, and 1.0 for the meniscus. The 35 paired measurements showed excellent agreement with statistical significance (P < 0.05). The 3D UTE MRI provides imaging of short T2 tissues which cannot be visualized by conventional MRI. Using weighted subtractions with optimal weighting values, each tissue can be optimally depicted by overcoming the reduced T2 contrast.