National Magnetic Resonance Research Center (UMRAM)

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Open Access
Intravascular MR-monitored balloon angioplasty: An in vivo feasibility study
(Elsevier Inc., 1998) Yang, Xiaoming; Bolster Jr., B. D.; Kraitchman, D. L.; Atalar, Ergin
PURPOSE: To develop a new method for monitoring balloon angioplasty by using an intravascular magnetic resonance (MR) imaging technique. MATERIALS AND METHODS: Nine New Zealand White rabbits were used: seven for technique refinement, including surgery, device insertion, stenosis creation, and MR protocol development; and two for the final MR imaging of the balloon angioplasty. The in vivo experimental method involved insertion of a catheter antenna and a balloon catheter, via femoral arteriotomies bilaterally, into the target site of the upper abdominal aorta, where a stenosis was artificially created by binding a plastic cable tie. Then, the entire process of the dilation of the stenosis with balloon inflation was monitored under MR fluoroscopy. RESULTS: Catheter insertions were successful, and a 5-mm-long stenosis of the aorta was produced in all nine rabbits. Eight complete balloon angioplasty procedures were satisfactorily monitored and recorded, showing clearly the stenosis of the aorta at the beginning of the procedure, the dilation of the stenosis during the balloon inflation, and the complete opening of the stenosis after balloon dilation. CONCLUSION: Preliminary results of in vivo balloon angioplasty monitored with intravascular MR imaging are presented. MR fluoroscopy, based on the intravascular MR imaging technique, may represent a potential alternative to x-ray fluoroscopy for guiding interventional treatment of cardiovascular diseases.
Open Access
SSFP-based MR thermometry
(John Wiley & Sons, 2004) Paliwal, V.; El-Sharkawy, A.-M.; Du, X.; Yang, X.; Atalar, Ergin
Of the various techniques employed to quantify temperature changes by MR, proton resonance frequency (PRF) shift-based phase-difference imaging (PDI) is the most accurate and widely used. However, PDI is associated with various artifacts. Motivated by these limitations, we developed a new method to monitor temperature changes by MRI using the balanced steady-state free precession (balanced-SSFP) pulse sequence. Magnitude images obtained with the SSFP pulse sequence were used to find the PRF shift, which is proportional to temperature change. Spatiotemporal temperature maps were successfully reconstructed with this technique in gel phantom experiments and a rabbit model. The results show that the balanced-SSFP-based method is a promising new technique for monitoring temperature.
Open Access
Evaluation of internal MRI coils using ultimate intrinsic SNR
(John Wiley & Sons, 2004) Çelik, H.; Eryaman, Y.; Altıntaş, A.; Abdel-Hafez, I. A.; Atalar, Ergin
The upper bounds of the signal-to-noise ratio (also known as the "ultimate intrinsic signal-to-noise ratio" (UISNR)) for internal and external coils were calculated. In the calculation, the body was modeled as a dielectric cylinder with a small coaxial cylindrical cavity in which internal coils could be placed. The calculated UISNR values can be used as reference solutions to evaluate the performance of internal MRI coils. As examples, we evaluated the performance of a loopless antenna and an endourethral coil design by comparing their ISNR with the UISNR.
Open Access
Magnetic resonance imaging–guided coronary interventions
(John Wiley & Sons, 2004) Tsekos, N. V.; Ergin, A.; Li, D.; Omary, R. A.; Serfaty, J.-M.; Woodard, P. K.
Magnetic resonance imaging (MRI) guidance for coronary interventions offers potential advantages over conventional x‐ray angiography. Advantages include the use of nonionizing radiation, combined assessment of anatomy and function, and three‐dimensional assessment of the coronary arteries leading to the myocardium. These advantages have prompted a series of recent studies in this field. Real‐time coronary MR angiography, with low‐dose catheter‐directed intraarterial (IA) infusion of contrast media, has achieved in‐plane spatial resolution as low as 0.8 × 0.8 mm2 and temporal resolution as short as 130 msec per image. Catheter‐based IA injection of contrast agent has proven useful in the collection of multislice and three‐dimensional images, not only for coronary intervention guidance, but also in the assessment of regional myocardial perfusion fed by the affected vessel. Actively visible guidewires and guiding catheters, based on the loopless antenna concept, have been effectively used to negotiate tortuous coronary vessels during catheterization, permitting placement of coronary angioplasty balloon catheters. Passive tracking approaches have been used to image contrast agent–filled coronary catheters and to place susceptibility‐based endovascular stents. Although the field is in its infancy, these early results demonstrate the feasibility for performing MRI‐guided coronary interventions. Although further methodological and technical developments are required before these methods become clinically applicable, we anticipate that MRI someday will be included in the armamentarium of techniques used to diagnose and treat coronary artery disease.
Open Access
MR-trackable intramyocardial injection catheter
(John Wiley & Sons, 2004) Karmarkar, P. V.; Kraitchman, D. L.; Izbudak, I.; Hofmann, L. V.; Amado, L. C.; Fritzges, D.; Young, R.; Pittenger, M.; Bulte, J. W. M.; Atalar, Ergin
There is growing interest in delivering cellular agents to infarcted myocardium to prevent postinfarction left ventricular remodeling. MRI can be effectively used to differentiate infarcted from healthy myocardium. MR-guided delivery of cellular agents/therapeutics is appealing because the therapeutics can be precisely targeted to the desired location within the infarct. In this study, a steerable intramyocardial injection catheter that can be actively tracked under MRI was developed and tested. The components of the catheter were arranged to form a loopless RF antenna receiver coil that enabled active tracking. Feasibility studies were performed in canine and porcine myocardial infarction models. Myocardial delayed-enhancement (MDE) imaging identified the infarcted myocardium, and real-time MRI was used to guide left ventricular catheterization from a carotid artery approach. The distal 35 cm of the catheter was seen under MRI with a bright signal at the distal tip of the catheter. The catheter was steered into position, the distal tip was apposed against the infarct, the needle was advanced, and a bolus of MR contrast agent and tissue marker dye was injected intramyocardially, as confirmed by imaging and post-mortem histology. A pilot study involving intramyocardial delivery of magnetically labeled stem cells demonstrated the utility of the active injection catheter system.
Open Access
System for prostate brachytherapy and biopsy in a standard 1.5 T MRI scanner
(John Wiley & Sons, 2004) Susil, R.C.; Camphausen, K.; Choyke, P.; McVeigh, E. R.; Gustafson, G. S.; Ning, H.; Miller, R. W.; Atalar, Ergin; Coleman, C. N.; Ménard, C.
A technique for transperineal high-dose-rate (HDR) prostate brachytherapy and needle biopsy in a standard 1.5 T MRI scanner is demonstrated. In each of eight procedures (in four patients with intermediate to high risk localized prostate cancer), four MRI-guided transperineal prostate biopsies were obtained followed by placement of 14-15 hollow transperineal catheters for HDR brachytherapy. Mean needle-placement accuracy was 2.1 mm, 95% of needle-placement errors were less than 4.0 mm, and the maximum needle-placement error was 4.4 mm. In addition to guiding the placement of biopsy needles and brachytherapy catheters, MR images were also used for brachytherapy treatment planning and optimization. Because 1.5 T MR images are directly acquired during the interventional procedure, dependence on deformable registration is reduced and online image quality is maximized.
Open Access
Evaluation of MR/Fluoroscopy–guided portosystemic shunt creation in a swine model
(Elsevier Inc., 2006) Arepally, A.; Karmarkar, P. V.; Qian, D.; Barnett, B.; Atalar, Ergin
PURPOSE: To evaluate three different percutaneous portosystemic shunts created with magnetic resonance (MR) imaging and fluoroscopy guidance in a swine model. MATERIALS AND METHODS: In stage 1 of the experiment, an active MR intravascular needle system was created for needle tracking and extracaval punctures. Twenty inferior vena cava (IVC)/superior mesenteric vein (SMV)/portal vein (PV) punctures were performed in 10 swine (weight, 40-45 kg) in a 1.5-T short-bore interventional MR imager. With use of a real-time MR imaging sequence, the needle was guided through the IVC and into the SMV or PV (N = 20 punctures). After confirmation, a wire was advanced into the portal venous system under MR imaging guidance (N = 20). In stage 2, animals were transferred to the radiographic fluoroscopy suite for deployment of shunts. Three different shunts were evaluated in this study: (i) a commercial stent-graft, (ii) a prototype bridging stent, and (iii) a prototype nitinol vascular anastomotic device. Postprocedural necropsy was performed in all animals. RESULTS: Successful MR-guided IVC/SMV punctures were performed in all 20 procedures (100%). All three shunts were deployed. Stent-grafts had the poorest mechanism for securing a shunt. The vascular anastomotic device and the bridging stent had more secure anchoring mechanisms but also had higher technical failure rates (50% and 40%, respectively). When deployed successfully, the vascular anastomotic device resulted in no bleeding at the sites of punctures at necropsy. CONCLUSION: Percutaneous shunts and vascular anastomoses between the portal mesenteric venous system and IVC were successfully created with use of a combination of MR imaging and conventional fluoroscopy for guidance.
Open Access
Electrical circuit modeling of surface structures for X-ray photoelectron spectroscopic measurements
(Elsevier BV * North-Holland, 2008) Tasci, T. O.; Atalar, Ergin; Demirok, U. K.; Süzer, Şefik
We model the X-ray photoelectron spectrometer and the sample with lumped electrical circuit elements, and simulate various types of conditions using a widely used computer program (PSpice) and compare the results with experimental measurements. By using the electrical model simulations, the surface voltage and the spectrum can be estimated under various types of external voltage stimuli, and the zero potential condition can be predicted accurately for obtaining a truly uncharged spectrum. Additionally, effects of several charging mechanisms (taking place during XPS measurements) on the surface potential could easily be assessed. Finally, the model enables us to find electrical properties, like resistance and capacitance of surface structures, under X-ray and low-energy electron exposure.
Open Access
Object rigidity and reflectivity identification based on motion analysis
(IEEE, 2010) Zang, D.; Schrater P.R.; Doerschner, Katja
Rigidity and reflectivity are important properties of objects, identifying these properties is a fundamental problem for many computer vision applications like motion and tracking. In this paper, we extend our previous work to propose a motion analysis based approach for detecting the object's rigidity and reflectivity. This approach consists of two steps. The first step aims to identify object rigidity based on motion estimation and optic flow matching. The second step is to classify specular rigid and diffuse rigid objects using structure from motion and Procrustes analysis. We show how rigid bodies can be detected without knowing any prior motion information by using a mutual information based matching method. In addition, we use a statistic way to set thresholds for rigidity classification. Presented results demonstrate that our approach can efficiently classify the rigidity and reflectivity of an object. © 2010 IEEE.
Open Access
Unsupervised tissue image segmentation through object-oriented texture
(IEEE, 2010) Tosun, Akif Burak; Sokmensuer, C.; Gündüz-Demir, Çiğdem
This paper presents a new algorithm for the unsupervised segmentation of tissue images. It relies on using the spatial information of cytological tissue components. As opposed to the previous study, it does not only use this information in defining its homogeneity measures, but it also uses it in its region growing process. This algorithm has been implemented and tested. Its visual and quantitative results are compared with the previous study. The results show that the proposed segmentation algorithm is more robust in giving better accuracies with less number of segmented regions. © 2010 IEEE.
Open Access
Perceived glossiness in high dynamic range scenes
(Association for Research in Vision and Ophthalmology, 2010) Doerschner, K.; Maloney,Laurence T.; Boyaci, Hüseyin
We investigated how spatial pattern, background, and dynamic range affect perceived gloss in brightly lit real scenes. Observers viewed spherical objects against uniform backgrounds. There were three possible objects. Two were black matte spheres with circular matte white dots painted on them (matte-dot spheres). The third sphere was painted glossy black (glossy black sphere). Backgrounds were either black or white matte, and observers saw each of the objects in turn on each background. Scenes were illuminated by an intense collimated source. On each trial, observers matched the apparent albedo of the sphere to an albedo reference scale and its apparent gloss to a gloss reference scale. We found that mattedot spheres and the black glossy sphere were perceived as glossy on both backgrounds. All spheres were judged to be significantly glossier when in front of the black background. In contrast with previous research using conventional computer displays, we find that background markedly affects perceived gloss. This finding is surprising because darker surfaces are normally perceived as glossier (F. Pellacini, J. A. Ferwerda, & D. P. Greenberg, 2000). We conjecture that there are cues to surface material signaling glossiness present in high dynamic range scenes that are absent or weak in scenes presented using conventional computer displays.
Open Access
Estimating the glossiness transfer function induced by illumination change and testing its transitivity
(Association for Research in Vision and Ophthalmology, 2010) Doerschner, K.; Boyacı, Hüseyin; Maloney, Laurence T.
The light reflected from a glossy surface depends on the reflectance properties of that surface as well as the flow of light in the scene, the light field. We asked four observers to compare the glossiness of pairs of surfaces under two different realword light fields, and used this data to estimate a transfer function that captures how perceived glossiness is remapped in changing from one real-world light field to a second. We wished to determine the form of the transfer function and to test whether for any set of three light fields the transfer function from light field 1 to light field 2 and the transfer function from light field 2 to light field 3 could be used to predict the glossiness transfer function from light field 1 to light field 3. Observers' estimated glossiness transfer functions for three sets of light fields were best described by a linear model. The estimated transfer functions exhibited the expected transitivity pattern for three out of four observers. The failure of transitivity for one observer, while significant, was less than 12.5% of the gloss range.
Open Access
Perceptual grouping-dependent lightness processing in human early visual cortex
(Association for Research in Vision and Ophthalmology, 2010) Boyaci, H.; Fang, F.; Murray, S. O.; Kersten, D.
Lightness, the perceived relative achromatic reectance of a surface, depends strongly on the context within which the surface is viewed. Modest changes in the two-dimensional conguration or three-dimensional scene geometry may lead to profound variations in lightness even though the surface luminance remains constant. Despite recent progress, we are far from a complete understanding of how various aspects of spatial context affect lightness processing in the cortex. Here we use a novel stimulus to show that perceptual grouping through occluders can affect lightness. We first report behavioral results showing how lightness across occlusion depends on spatially distant image features, including luminance and contrast. Next using functional magnetic resonance imaging (fMRI) we show that human early visual cortex responds strongly to occlusion-dependent lightness variations with little or no attention. These results suggest that elements of three-dimensional scene interpretation play a role in early cortical processing of lightness.
Open Access
Reduction of implant RF heating through modification of transmit coil electric field
(WILEY, 2010-12-08) Eryaman, Y.; Akin, B.; Atalar, Ergin
In this work, we demonstrate the possibility to modify the electric-field distribution of a radio frequency (RF) coil to generate electric field-free zones in the body without significantly altering the transmit sensitivity. Because implant heating is directly related to the electric-field distribution, implant-friendly RF transmit coils can be obtained by this approach. We propose a linear birdcage transmit coil with a zero electric-field plane as an example of such implant-friendly coils. When the zero electric-field plane coincides with the implant position, implant heating is reduced, as we demonstrated by the phantom experiments. By feeding RF pulses with identical phases and shapes but different amplitudes to the two orthogonal ports of the coil, the position of the zero electric-field plane can also be adjusted. Although implant heating is reduced with this method, a linear birdcage coil results in a whole-volume average specific absorption rate that is twice that of a quadrature birdcage coil. To solve this issue, we propose alternative methods to design implant-friendly RF coils with optimized electromagnetic fields and reduced whole-volume average specific absorption rate. With these methods, the transmit field was modified to reduce RF heating of implants and obtain uniform transmit sensitivity.
Open Access
Homozygosity mapping and targeted genomic sequencing reveal the game responsible for cerebellar hypoplasia and quadrupedal locomotion in a consanguineous kindred
(Cold Spring Harbor Laboratory Press, 2011) Gulsuner, Süleyman; Tekinay, Ayşe Begüm; Doerschner, Katja; Boyaci, Hüseyin; Bilguvar, K.; Ünal, Hilal; Örs, Aslıhan; Onat, O. Emre; Atalar, Ergin; Basak, A. N.; Topaloglu, H.; Kansu, T.; Tan, M.; Tan, U.; Gunel, M.; Özçelik, Tayfun
The biological basis for the development of the cerebro-cerebellar structures required for posture and gait in humans is poorly understood. We investigated a large consanguineous family from Turkey exhibiting an extremely rare phenotype associated with quadrupedal locomotion, mental retardation, and cerebro-cerebellar hypoplasia, linked to a 7.1-Mb region of homozygosity on chromosome 17p13.1-13.3. Diffusion weighted imaging and fiber tractography of the patients' brains revealed morphological abnormalities in the cerebellum and corpus callosum, in particular atrophy of superior, middle, and inferior peduncles of the cerebellum. Structural magnetic resonance imaging showed additional morphometric abnormalities in several cortical areas, including the corpus callosum, precentral gyrus, and Brodmann areas BA6, BA44, and BA45. Targeted sequencing of the entire homozygous region in three affected individuals and two obligate carriers uncovered a private missense mutation, WDR81 p.P856L, which cosegregated with the condition in the extended family. The mutation lies in a highly conserved region of WDR81, flanked by an N-terminal BEACH domain and C-terminal WD40 beta-propeller domains. WDR81 is predicted to be a transmembrane protein. It is highly expressed in the cerebellum and corpus callosum, in particular in the Purkinje cell layer of the cerebellum. WDR81 represents the third gene, after VLDLR and CA8, implicated in quadrupedal locomotion in humans.
Open Access
Peptide functionalized superparamagnetic iron oxide nanoparticles as MRI contrast agents
(The Royal Society of Chemistry, 2011) Sulek, S.; Mammadov, B.; Mahcicek, D. I.; Sozeri, H.; Atalar, Ergin; Tekinay, A. B.; Güler, Mustafa O.
Magnetic resonance imaging (MRI) attracts great attention in cellular and molecular imaging due to its non-invasive and multidimensional tomographic capabilities. Development of new contrast agents is necessary to enhance the MRI signal in tissues of interest. Superparamagnetic iron oxide nanoparticles (SPIONs) are used as contrast agents for signal enhancement as they have revealed extraordinary magnetic properties at the nanometre size and their toxicity level is very low compared to other commercial contrast agents. In this study, we developed a new method to functionalize the surface of SPIONs. Peptide amphiphile molecules are used to coat SPIONs non-covalently to provide water solubility and to enhance biocompatibility. Superparamagnetic properties of the peptide-SPION complexes and their ability as contrast agents are demonstrated. In vitro cell culture experiments reveal that the peptide-SPION complexes are biocompatible and are localized around the cells due to their peptide coating.
Open Access
Visual motion and the perception of surface material
(Cell Press, 2011) Doerschner, K.; Fleming, R. W.; Yilmaz, O.; Schrater, P. R.; Hartung, B.; Kersten, D.
Many critical perceptual judgments, from telling whether fruit is ripe to determining whether the ground is slippery, involve estimating the material properties of surfaces. Very little is known about how the brain recognizes materials, even though the problem is likely as important for survival as navigating or recognizing objects. Though previous research has focused nearly exclusively on the properties of static images [1-16], recent evidence suggests that motion may affect the appearance of surface material [17-19]. However, what kind of information motion conveys and how this information may be used by the brain is still unknown. Here, we identify three motion cues that the brain could rely on to distinguish between matte and shiny surfaces. We show that these motion measurements can override static cues, leading to dramatic changes in perceived material depending on the image motion characteristics. A classifier algorithm based on these cues correctly predicts both successes and some striking failures of human material perception. Together these results reveal a previously unknown use for optic flow in the perception of surface material properties.
Open Access
Improving RF safety in MRI by modifying the electric field distribution
(IEEE, 2011) Eryaman, Yiğitcan; Atalar, Ergin
In this work we demonstrate that the radiofrequency (RF) electric field in magnetic resonance imaging (MRI) can be modified in order to enhance patient safety. The heating of metallic devices in MRI is directly related to electric field distribution. On the other hand the MR image homogeneity is related to forward polarized component of the magnetic field (transmit sensitivity). In order to prevent heating, electric field-free zones should be generated in the body without significantly altering the transmit sensitivity. For this purpose the linearly polarized birdcage coil is proposed as a metallic device friendly MRI coil. The zero electric field plane of the linear birdcage coil is coincided with the location of the metallic device and the heating is reduced as shown by simulations and experiments. One disadvantage of this approach is, the linear coils generate twice as much whole body average SAR when compared to quadrature birdcage coils. In order to solve this problem simulations are performed to find electromagnetic field solutions with reduced average SAR and uniform transmit sensitivity. © 2011 IEEE.
Open Access
Analytic expressions for the ultimate intrinsic signal-to-noise ratio and ultimate intrinsic specific absorption rate in MRI
(Wiley, 2011-03-09) Kopanoglu, E.; Erturk, V. B.; Atalar, Ergin
The ultimate intrinsic signal-to-noise ratio is the highest possible signal-to-noise ratio, and the ultimate intrinsic specific absorption rate provides the lowest limit of the specific absorption rate for a given flip angle distribution. Analytic expressions for ultimate intrinsic signal-to-noise ratio and ultimate intrinsic specific absorption rate are obtained for arbitrary sample geometries. These expressions are valid when the distance between the point of interest and the sample surface is smaller than the wavelength, and the sample is homogeneous. The dependence on the sample permittivity, conductivity, temperature, size, and the static magnetic field strength is given in analytic form, which enables the easy evaluation of the change in signal-to-noise ratio and specific absorption rate when the sample is scaled in size or when any of its geometrical or electrical parameters is altered. Furthermore, it is shown that signal-to-noise ratio and specific absorption rate are independent of the permeability of the sample. As a practical case and a solution example, a uniform, circular cylindrically shaped sample is studied. Copyright
Open Access
Reverse polarized inductive coupling to transmit and receive radiofrequency coil arrays
(Wiley, 2011-06-07) Celik, H.; Atalar, Ergin
In this study, the reverse polarization method is implemented using transmit and receive arrays to improve the visibility of the interventional devices. Linearly polarized signal sources-inductively and receptively coupled radiofrequency coils-are used in the experimental setups to demonstrate the ability of the method to separate these sources from a forward polarized anatomy signal. Two different applications of the reverse polarization method are presented here: (a) catheter tracking and (b) fiducial marker visualization, in both of which transmit and receive arrays are used. The performance of the reverse polarization method was further tested with phantom and volunteer studies, and the results proved the feasibility of this method with transmit and receive arrays.