Optimizing MRI sequences and images for MRI-based stereotactic radiosurgery treatment planning

AimDevelopment of MRI sequences and processing methods for the production of images appropriate for direct use in stereotactic radiosurgery (SRS) treatment planning.BackgroundMRI is useful in SRS treatment planning, especially for patients with brain lesions or anatomical targets that are poorly distinguished by CT, but its use requires further refinement. This methodology seeks to optimize MRI sequences to generate distortion-free and clinically relevant MR images for MRI-only SRS treatment planning.Materials and methodsWe used commercially available SRS MRI-guided radiotherapy phantoms and eight patients to optimize sequences for patient imaging. Workflow involved the choice of correct MRI sequence(s), optimization of the sequence parameters, evaluation of image quality (artifact free and clinically relevant), measurement of geometrical distortion, and evaluation of the accuracy of our offline correction algorithm.ResultsCT images showed a maximum deviation of 1.3 mm and minimum deviation of 0.4 mm from true fiducial position for SRS coordinate definition. Interestingly, uncorrected MR images showed maximum deviation of 1.2 mm and minimum of 0.4 mm, comparable to CT images used for SRS coordinate definition. After geometrical correction, we observed a maximum deviation of 1.1 mm and minimum deviation of only 0.3 mm.ConclusionOur optimized MRI pulse sequences and image correction technique show promising results; MR images produced under these conditions are appropriate for direct use in SRS treatment planning.     

Recognition of brain tumors in MRI images using texture analysis

ObjectivesBrain neoplasms or intracranial tumors, which are more common in older adults, can affect individuals of any age including pediatric and children. Exposure to carcinogenic agents including ionizing radiation and family history is one of the main causes of the disease. Early diagnosis is crucial to avoid prolonged. patients' suffering. The aim of the study was to efficiently recognize the brain tumors from the other brain tissues which include grey and white matter as well as cerebrospinal fluid (CSF).Materials and methodsThis study was performed using axial, sagittal and coronal views for fifty brain tumor patients randomly selected from a set of 200 patients, with a “control” set consisting of images showing no sign of disease; and the “test” brain MRI images for patients diagnosed with brain tumor. The study includes both genders with age ranging from 18 years to 83 years old, (56.5 ± 17.2). The brain images were acquired using a standard head coil Philips Intera 1.5 Tesla machine (USA). The thickness of each section in the entire sequence was 8 mm. Acquisition of T2-weighted and T1-weighted were performed. Interactive Data Language software was used to analyze the data.ResultsThe results of this study showed that: the overall accuracy of classification process was 94.8%, and for the tumor; the sensitivity was 97.3%. White matter and grey matter showed a classification accuracy of 95.7% and 89.7% and for CSF the accuracy was 94.3%.ConclusionThe results showed that brain tumor can be classified successfully and delineated using texture analysis with minimum efforts and with high accuracy for brain tumors.     

帕金森病的MRI应用价值的研究

目的：探讨帕金森病（Parkinson＇s disease,PD）常规MRI的影像学表现特点和在常规MRI上测量黑质致密带（pars compacta of substantia nigra,SNc）宽度对PD的评估价值。方法：对90例PD患者（Hoehn-Yahr分级为Ⅰ-Ⅱ级57例、Ⅲ级18例、Ⅳ级15例）、60例年龄匹配的健康对照者进行MRI检查,分析PD患者的常规MRI影像学表现,对比分析PD组和对照组中MRI的白质高信号（包括侧脑室周围和半卵圆中心的白质高信号）的发生率,并对比分析PD组和对照组的SNc宽度。结果：PD组比对照组侧脑室周围白质高信号的发生率明显增高（P〈0．01）,但PD组的半卵圆中心白质高信号的发生率与对照组无明显差异;PD组比对照组SNc宽度明显变窄,并且PD患者随病情加重其SNc宽度更加变窄。结论：PD常规MRI的影像学表现不具有诊断上的特异性,但在常规MRI上侧脑室周围白质高信号的观察和SNc宽度的测量对PD的评估具有临床应用价值。     

Efficient and Reliable Assessment of the Maximum Local Tissue Temperature Increase at the Electrodes of Medical Implants under MRI Exposure

Standard risk evaluations posed by medical implants during magnetic resonance imaging (MRI) includes (i) the assessment of the total local electromagnetic (EM) power (P) absorbed in the vicinity of the electrodes and (ii) the translation of P into a local in vivo tissue temperature increase ?T (P2?T) in animal experiments or simulations. We investigated the implant/tissue modeling requirements and associated uncertainties by applying full‐wave EM and linear bioheat solvers to different implant models, incident field conditions, electrode configurations, and tissue models. Results show that the magnitude of the power is predominately determined by the lead, while the power distribution, and the P2?T conversion, is determined by the electrode and surrounding tissues. P2?T is strongly dependent on the size of the electrode, tissue type in contact with the electrode, and tissue inhomogeneity (factor of >2 each) but less on the modeling of the lead (<±10%) and incident field distribution along the lead (<±20%). This was confirmed by means of full‐wave simulations performed with detailed high‐resolution anatomical phantoms exposed to two commonly used MRI clinical scenarios (64 and 128 MHz), resulting in differences of less than 6%. For the determination of P2?T, only the electrode and surrounding tissues must be modeled in great detail, whereas the lead can be modeled as a computationally efficient simplified structure exposed to a uniform field. The separate assessments of lead and electrode reduce the overall computational effort by several orders of magnitude. The errors introduced by this simplification can be considered by uncertainty terms. Bioelectromagnetics. 2019;40:422–433. © 2019 Bioelectromagnetics Society.     

Age at death determination by means of femoral frequency of secondary osteons

A statistical model for the estimation of the age at death is defined and tested to evaluate its performance. It is characterized by the probability of the femoral frequency of secondary osteons for any given age, that we compute by means of 28 scheletons of Italian subjects. In a standard case we obtain good evalutations of the methods, while in practice it can be used according to the objectives of the particular investigation. Moreover other surveys could easily be added to our data in order to obtain a more powerfool tool.     

Geometric inaccuracy and co-registration errors for CT,DynaCT and MRI images used in robotic stereotactic radiosurgery treatment planning

PurposeTo measure the combined errors due to geometric inaccuracy and image co-registration on secondary images (dynamic CT angiography (dCTA), 3D DynaCT angiography (DynaCTA), and magnetic resonance images (MRI)) that are routinely used to aid in target delineation and planning for stereotactic radiosurgery (SRS).MethodsThree phantoms (one commercial and two in-house built) and two different analysis approaches (commercial and MATLAB based) were used to quantify the magnitude of geometric image distortion and co-registration errors for different imaging modalities within CyberKnife’s MultiPlan treatment planning software. For each phantom, the combined errors were reported as a mean target registration error (TRE). The mean TRE’s for different intramodality imaging parameters (e.g., mAs, kVp, and phantom set-ups) and for dCTA, DynaCTA, and MRI systems were measured.ResultsOnly X-ray based imaging can be performed with the commercial phantom, and the mean TRE ± standard deviation values were large compared to the in-house analysis using MATLAB. With the 3D printed phantom, even drastic changes in treatment planning CT imaging protocols did not greatly influence the mean TRE (<0.5 mm for a 1 mm slice thickness CT). For all imaging modalities, the largest mean TRE was found on DynaCT, followed by T2-weighted MR images (albeit all <1 mm).ConclusionsThe user may overestimate the mean TRE if the commercial phantom and MultiPlan were used solely. The 3D printed phantom design is a sensitive and suitable quality assurance tool for measuring 3D geometric inaccuracy and co-registration errors across all imaging modalities.     

SmProt: A Reliable Repository with Comprehensive Annotation of Small Proteins Identified from Ribosome Profiling

Small proteins specifically refer to proteins consisting of less than 100 amino acids translated from small open reading frames (sORFs), which were usually missed in previous genome annotation. The significance of small proteins has been revealed in current years, along with the discovery of their diverse functions. However, systematic annotation of small proteins is still insufficient. SmProt was specially developed to provide valuable information on small proteins for scientific community. Here we present the update of SmProt, which emphasizes reliability of translated sORFs, genetic variants in translated sORFs, disease-specific sORF translation events or sequences, and remarkably increased data volume. More components such as non-ATG translation initiation, function, and new sources are also included. SmProt incorporated 638,958 unique small proteins curated from 3,165,229 primary records, which were computationally predicted from 419 ribosome profiling (Ribo-seq) datasets or collected from literature and other sources from 370 cell lines or tissues in 8 species (Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster, Danio rerio, Saccharomyces cerevisiae, Caenorhabditis elegans, and Escherichia coli). In addition, small protein families identified from human microbiomes were also collected. All datasets in SmProt are free to access, and available for browse, search, and bulk downloads at http://bigdata.ibp.ac.cn/SmProt/.     

Reliable simulations of the human proximal femur by high-order finite element analysis validated by experimental observations

Background: The mechanical response of patient-specific bone to various load conditions is of major clinical importance in orthopedics. Herein we enhance the methods presented in Yosibash et al. [2007. A CT-based high-order finite element analysis of the human proximal femur compared to in-vitro experiments. ASME Journal of Biomechanical Engineering 129(3), 297–309.] for the reliable simulations of the human proximal femur by high-order finite elements (FEs) and validate the simulations by experimental observations.

Method of approach: A fresh-frozen human femur was scanned by quantitative computed tomography (QCT) and thereafter loaded (in vitro experiments) by a quasi-static force of up to 1250 N. QCT scans were manipulated to generate a high-order FE bone model with distinct cortical and trabecular regions having inhomogeneous isotropic elastic properties with Young's modulus represented by continuous spatial functions. Sensitivity analyses were performed to quantify parameters that mostly influence the mechanical response. FE results were compared to displacements and strains measured in the experiments.

Results: Young moduli correlated to QCT Hounsfield Units by relations in Keyak and Falkinstein [2003. Comparison of in situ and in vitro CT scan-based finite element model predictions of proximal femoral fracture load. Medical Engineering and Physics 25, 781–787.] were found to provide predictions that match the experimental results closely. Excellent agreement was found for both the displacements and strains. The presented study demonstrates that reliable and validated high-order patient-specific FE simulations of human femurs based on QCT data are achievable for clinical computer-aided decision making.     

Study of femoral torsion during prenatal growth: interpretations associated with the effects of intrauterine pressure

The developing fetus is protected from external environmental influences by maternal tissues. However, these structures have a limited elasticity, such that the fetus must grow in a confined space, constraining its size at the end of pregnancy. Can these constraints modify the morphology of the fetal skeleton? The intensity of these constraints increases between 5 months and birth, making it the most appropriate period to address this question. A sample of 89 fetal femora was analyzed, and results provide evidence that during this period, the torsion of the femoral shaft (quantified by means of a new three‐dimensional method) increases gradually. Two explanations were considered: this increase could signal effects of constraints induced by the intrauterine cavity, developmental patterning, or some combination of these two. Different arguments tend to support the biomechanical explanation, rather than a programming pattern formation. Indeed, the identification of the femur as a first degree lever, created by the hyperflexion of the fetal lower limbs on the pelvis, could explain the increase in femoral shaft torsion during prenatal life. A comparison with femora of infants is in accordance with this mechanical interpretation, which is possible through bone modeling/remodeling. Although genetic and epigenetic mechanisms may regulate timing of fetal development, our data suggest that at birth, the fetal skeleton also has an intrauterine mechanical history through adaptive bone plasticity. Am J Phys Anthropol, 2011. © 2011Wiley‐Liss, Inc.     

Ultrasound-driven cardiac MRI

PurposeOne of the challenges of cardiac MR imaging is the compensation of respiratory motion, which causes the heart and the surrounding tissues to move. Commonly-used methods to overcome this effect, breath-holding and MR navigation, present shortcomings in terms of available acquisition time or need to periodically interrupt the acquisition, respectively. In this work, an implementation of respiratory motion compensation that obtains information from abdominal ultrasound and continuously adapts the imaged slice position in real time is presented.MethodsA custom workflow was developed, comprising an MR-compatible ultrasound acquisition system, a feature-motion-tracking system with polynomial predictive capability, and a custom MR sequence that continuously adapts the position of the acquired slice according to the tracked position. The system was evaluated on a moving phantom by comparing sharpness and image blurring between static and moving conditions, and in vivo by tracking the motion of the blood vessels of the liver to estimate the cardiac motion. Cine images of the heart were acquired during free breathing.ResultsIn vitro, the predictive motion correction yielded significantly better results than non-predictive or non-corrected acquisitions (p ≪ 0.01). In vivo, the predictive correction resulted in an image quality very similar to the breath-hold acquisition, whereas the uncorrected images show noticeable blurring artifacts.ConclusionIn this work, the possibility of using ultrasound navigation with tracking for the real-time adaptation of MR imaging slices was demonstrated. The implemented technique enabled efficient imaging of the heart with resolutions that would not be feasible in a single breath-hold.     

Towards a patient-specific estimation of intra-operative femoral fracture risk

Abstract

Total Hip Arthroplasty requires pre-surgical evaluation between un-cemented and cemented prostheses. A Patient with intra-operative periprosthetic fracture and another with a successful outcome were recruited, and their finite element models were constructed by processing CT data, assuming elastic-plastic behavior of the bone as function of the local density. To resemble the insertion of the prosthesis into the femur, a fictitious thermal dilatation is applied to the broach volume. Strain-based fracture risk factor is estimated, depicting results in terms of the total mechanical strain expressed using a simple “traffic lights” color code to provide immediate, concise, and intelligible pre-operative information to surgeons.     

Fuzzy algorithms: Application to adipose tissue quantification on MR images

Metabolic syndrome, which is related to abdominal obesity, is a fast growing disease in our western countries. Its presence greatly increases the risk of developing cardiovascular diseases. The accumulation of visceral adipose tissue plays a key role in the development of the metabolic syndrome. The increase of waist circumference is one of the five criteria of the metabolic syndrome diagnosis. But this increase can be due to visceral or subcutaneous adipose tissues. And these adipose tissues do not play the same rule in metabolic syndrome. The purpose of this study was to develop software for automatic and reliable quantification of visceral and subcutaneous adipose tissues, to detect patient with high risk to develop metabolic syndrome and to follow the evolution of adipose tissue repartition after treatment. A gradient echo magnetic resonance (MR) technique is used, with a TE such that fat and water are opposed in phase. The developed process is based on two fuzzy algorithms. First, we fuzzy generalized clustering algorithms allow to merge pixels according to their intensities. Then, fuzzy connectedness algorithm allows to merge pixels according to cost function related to distance, gradient distance and intensities. A validation is performed with a comparison between expert results made by manual drawing and purpose-made software results. Our software provides an automatic and reliable method to segment visceral and subcutaneous adipose tissue and additionally avoids in some case the problem of inhomogeneity of signal intensity.     

Unsupervised clustering of fMRI and MRI time series

Unsupervised clustering represents a powerful technique for self-organized segmentation of biomedical image time series data describing groups of pixels exhibiting similar properties of local signal dynamics. The theoretical background is presented in the beginning, followed by several medical applications demonstrating the flexibility and conceptual power of these techniques. These applications range from functional MRI data analysis to dynamic contrast-enhanced perfusion MRI and breast MRI. For fMRI, these methods can be employed to identify and separate time courses of interest, along with their associated spatial patterns. When applied to dynamic perfusion MRI, they identify groups of voxels associated with time courses that are clinically informative and straightforward to interpret. In breast MRI, a segmentation of the lesion is achieved and in addition a subclassification is obtained within the lesion with regard to regions characterized by different MRI signal time courses. In the present paper, we conclude that unsupervised clustering techniques provide a robust method for blind analysis of time series image data in the important and current field of functional and dynamic MRI.     

Relationship between formation of the femoral bicondylar angle and trochlear shape: independence of diaphyseal and epiphyseal growth

During hominin evolution, an increase in the femoral bicondylar angle was the initial change that led to selection for protuberance of the lateral trochlear lip and the elliptical profile of the lateral condyle. No correlation is found during ontogeny between the degree of femoral obliquity and of the prominence of the lateral trochlear lip. Might there be a relationship with the elliptical profile of the lateral condyle? On intact femoral diaphyses of juvenile humans and great apes, we compared the anteroposterior length of the lateral and medial sides of the distal metaphysis. The two diaphyseal pillars remain equal during postnatal growth in great apes, while the growth of the lateral pillar far exceeds that of the medial pillar in humans. Increase in bicondylar angle is correlated with disproportionate anteroposterior lengthening of the lateral pillar. The increased anteroposterior length of the lateral side of the metaphysis would contribute to increasing the radius of the curvature of the lateral condyle, but not to the projection of the lateral trochlear lip. The similar neonatal and adult femoro‐patellar joint shape in humans prompted an assessment of the similarity during growth of the entire neonatal and adult epiphyses. We showed that the entire epiphysis undergoes drastic changes in proportions during postnatal growth. Finally, we emphasize the need to distinguish the cartilaginous phenotype and the ossified phenotype of the distal femoral epiphysis (and of any epiphysis) during postnatal growth. This crucial distinction applies to most postcranial bones, for they almost all develop following the process of endochondral ossification. Am J Phys Anthropol, 2006. © 2006 Wiley‐Liss, Inc.