News

We are very happy to announce that we have new youtube channel and Facebook page. Do not forget to subscribe/follow to get notifications and latest news.   Please click and check ↓ Youtube: https://www.youtube.com/channel/UCfPApPtAbIThLTTrbLYslWQ Facebook: https://www.facebook.com/bilkentUMRAM

Alireza Sadeghi Tarakameh has presented his PhD thesis titled ”Novel Techniques and Innovative Design for the RF Chain of Magnetic Resonance Imaging Scanners” on July 29, 2020.   Abstract In this dissertation, novel techniques and innovative designs are proposed to serve one of the main goals of MRI, which is achieving the best image quality by improving signal-to-noise ratio (SNR) while confined to the patient’s safety restrictions determined by specific absorption rate (SAR) limits. This dissertation comprises five different contributions to the field. First, the co-simulation method is accelerated using the equivalent circuit model of the intended coil and introduced as a compact novel technique for the fast design of transmit array (TxArray) coils. It is shown that the existing co-simulation method can be accelerated by more than 20-fold for different types of TxArray coils. In another study, a simple strategy is introduced for optimizing the topography of transmit elements to reduce the local SAR at ultra-high field (UHF, B0 ≥ 7 T) MRI. It is shown that the peak local 10g-averaged SAR can be reduced more than 20% for different types of transmit elements at two different field strengths (i.e., 7 T and 10.5 T). As another contribution, confining to the safety limits, the first in vivo human head images at 10.5 T is acquired. To ensure the safety of subjects, the EM simulation model of the radiofrequency (RF) coil is validated using an expanded validation workflow, then, safe RF power levels were calculated. In another study, a novel short dipole-like element with improved SAR performance, NODES antenna, is introduced which provides an opportunity to design highly-dense TxArray coils for UHF-MRI. Eventually, a nine-channel transmit/receive coil is built and human cadaver spine images are acquired at 10.5 T. In the final study, a new parameter, ultimate intrinsic SAR efficiency (UISARE), is introduced and calculated as the upper bound for SAR performance of the transmit coils at different field strengths. Overall, this dissertation proposes novel techniques and innovative structures for designing the TxArray coils, which mainly contribute to enhancing image quality and patient safety by improving SNR and reducing SAR.

Cemre Ariyurek has presented her phd thesis titled ” Frequency Response Analysis and Reconstruction Weighting Schemes for MR Elastography ” Abstract Magnetic resonance elastography (MRE) non-invasively and quantitatively assesses the elasticity of the in-vivo tissue. In MRE, shear waves are induced to the tissue by an actuator, while phase-contrast images are obtained by magnetic resonance imaging (MRI). Finally, elasticity maps are generated using displacement information carried by phase-contrast images. The direction and frequency of the induced shear waves could be crucial in MRE. Here, it is demonstrated by the frequency response MRE simulations that modes of the shear waves can be observed in the brain during MR elastography with high shear wave displacement values at the mode frequencies. High shear wave displacements,  10-20 times of the applied displacement, were observed at mode frequencies in phantom MRE experiments. The second part of the thesis focuses on weighting schemes to combine multiple elasticity maps reconstructed from data collected for different excitation frequencies and motion direction. A new weighting scheme, which maximizes the signal-to-noise ratio (SNR) of the final wave speed map, has been proposed for tomoelastography and Helmholtz inversions. For both inversion techniques, considering the noise on the complex MRI signal, the SNR of the reconstructed wave speed map was formulated by an analytical approach assuming a high SNR. Thus, with the proposed SNR weighting method, while not altering the accuracy or spatial resolution of the wave speed map, the SNR of the wave speed map has been improved by 2 and 1.6 times for tomoelastography and Helmholtz inversion, respectively.  The bias occurring for low SNR data cases was eliminated in tomoelastography and reduced in Helmholtz inversion with the proposed SNR-weighted reconstructions. Similarly, a strain-based weighting for MRE reconstruction has been introduced. Experimental results demonstrated that strain weights could prevent artifacts at the boundaries of encapsulated tumors or tissues with membranes; however, further examination is required. In this thesis, two independent contributions have been made to the field of magnetic resonance elastography. By showing the existence of modes of the shear waves in the body, new fronts are opened in the MRE actuation methods and safety. The improvements in the elasticity map inversions could lead to the routine use of MRE in clinical practice.    

Büşra Sarıgül, a master student at Ankara University (Department of Social Psychiatry), co-supervised by UMRAM faculty member Burcu Ayşen Ürgen successfully defended her master thesis! Her thesis is titled “Human Perception of Social Robots and Robotics Technology in Mental Health Services” and investigated audio-visual predictive processes in human-robot interaction.  The study that is part of Büşra’s thesis work was also presented as a Late Breaking Report at the ACM/IEEE International Conference on Human-Robot Interaction (HRI 2020) this year. Here is her abstract https://dl.acm.org/doi/abs/10.1145/3371382.3378302 and video presentation at HRI 2020 https://www.youtube.com/watch?v=Yxcn4Kilo6g&t.    

UMRAM MRI SCANNER HYGIENE PROCEDURES FOR COVID-19 The following hygiene procedures have been prepared for the safety of examiners, human participants and patients, our animal friends, and everyone working in UMRAM. Everyone MUST follow these rules strictly. Examiners, who do not follow these rules, will be BANNED from using the scanner. These rules are effective immediately and valid until further notice. Note that these are hygiene procedures, all other regular procedures MUST still be followed, such as checking for metals and MR-incompatible implants, and obtaining written informed consent forms. General procedures: In the rest of the document, MUST means an absolute requirement, SHOULD means a strong recommendation. “Scanner room” refers to the room where the scanner is located. “Scanner site” refers to the combination of the scanner room and the control room. ● The nature of examination (phantom, human, or animal) MUST be noted on the calendar when making a reservation. ● There MUST be at least a 1-hour gap between examinations that involve humans, animals or phantoms. ● Users will not be charged for the extra gap time. However, users MUST separately reserve those extra gap times on the calendar with the following note: “DO NOT USE SCANNER”. ● The gap time MUST not be used for any additional examination, analysis or a study of any other nature in the scanner site. Examiners MUST complete their examination and leave the scanner site by the end of their regular appointment. ● Examiners MUST NOT have any flu-like symptoms. A sample checklist is provided below. With a positive answer to ANY of the questions, the study MUST be postponed. ● Examiners MUST wear mouth and nose protection masks at all times. ● Examiners MUST wash and dry their hands before entering the scanner site. ● Upon entering the scanner site examiners MUST immediately disinfect their hands and MUST wear gloves. They MUST NOT touch any personal belongings afterward. ● Masks and gloves will be provided by UMRAM. ● All objects and surfaces that are used, touched, breathed on or otherwise interacted with MUST be disinfected at the end of the examination. Disinfecting agents will be provided by UMRAM. If you need help, our technical personnel will guide you for applying the disinfectants, so please ask them. ● All waste MUST be disposed of in the medical trash bin placed outside of the scanner site. Our technical personnel will help you locate the bin. ● Masks and gloves MUST NOT be reused and they MUST be renewed if removed. ● Gloves MUST be taken off in a way such that the outer surface of the glove does not touch the skin; turn the inner surface outwards so that one glove wraps the other. ● Personal belongings MUST NOT be placed on the console desk and chairs. They should be properly stored in cabinets or placed on the new desk placed in the scanner site. ● There MUST NOT be any eating or drinking, including water. Human participants or patients may be allowed to take their exam-related medicine if necessary. Disposable cups and/or containers MUST be used for this. ● There SHOULD NOT be more than two examiners at the scanner site unless the nature of the examination requires more than two examiners. ● Examiners SHOULD preserve a distance of 1.5m between them. ● Examiners SHOULD wear long clothing. ● All surfaces, e.g. the bed, head cushions, that the human participants, patients, or animals will contact MUST be appropriately covered. ● Examiners, who need to wash and disinfect their hands frequently, are advised to use skincare products. Human participant and patient (HPP) procedures: ● HPPs MUST be contacted beforehand and it MUST be ensured that they do not have any flu-like symptoms. A sample checklist is provided below. With a positive answer to ANY of the questions the examination MUST be postponed. ● There MUST be at least a 4-hour gap between the examinations of two HPPs, even if they are related to the same study. ● External HPPs MUST be met outside the building. ● HPPs’ body temperature MUST be measured before allowing them inside the building. A measurement device will be provided by UMRAM. ● HPPs MUST wear a mask before entering the building. If the HPP will wear a mask during examination, and if the mask has a metal part, it can create artifacts in MRI images. If this is a concern, ask the HPP to remove the metal part of their mask before entering the building. ● HPPs MUST be accompanied into the bathroom to wash and dry their hands. ● HPPs MUST be accompanied to the scanner site. ● Only one HPP at a time MUST be admitted into the scanner site. ● HPPs MUST remove all belongings and safely store them once inside the scanner site. ● HPPs MUST wear a medical gown. These gowns will be provided by UMRAM. The gown can be worn over HPPs’ clothes. ● HPPs MUST be guided to disinfect their hands and advised not to touch anything after disinfection. ● HPPs SHOULD bring their signed consent form if possible. If this is not possible HPPs SHOULD be provided with the form in the scanner site. The form SHOULD be signed on the new desk placed in the scanner site. HPPs SHOULD use their own pen to sign the papers. If they do not have a pen they SHOULD be provided with a disinfected pen. ● If needed, an accompanying person may accompany the HPP into the scanner site. Other visitors MUST remain in the waiting lounge and follow the rules of social distance ● Maximum possible distance between the examiner and HPP MUST be preserved at all times, including while positioning the HPP on the bed and attaching the coils. Only one examiner SHOULD prepare the HPP and send inside the scanner bore. ● HPPs SHOULD not be allowed to enter the part of the scanner site where the console desk is located. This part SHOULD be reserved for the examiners only. ● HPPs SHOULD keep their masks on during the examination. If this is not possible, for example, to avoid artifacts or head movements, HPPs’ masks may be removed just before positioning them on the bed. ● HPPs MUST put on earplugs themselves. ● In case the HPP cannot wear a mask due to the nature of the study, the examiners SHOULD exercise extra caution and are advised to wear a full-face protective transparent screen. Those screens will be provided by UMRAM. Flu-symptom checklist: 1. Have you had a fever in the past 14 days? Yes/No 2. Have you had a dry cough in the past 14 days? Yes/No 3. Have you had any acute muscle problems/limb pain in the past 14 days? Yes/No 4. Have you had an acute headache in the past 14 days? (If you frequently experience headaches, answer “No” if the headache felt as usual) Yes/No 5. Have you had any sudden changes in taste, flavor or olfactory sensation in the past 14 days? Yes/No 6. Have you had acute diarrhea in the past 14 days? Yes/No 7. Have you been in contact with other suspected cases in the past 14 days? Yes/No 8. Have you been abroad in the last 14 days? Yes/No Animal Examination Procedures: ● Animals SHOULD be admitted to the scanner room through the side door. ● There MUST be a 1-hour gap after an animal study. There may be more than 1 animal subject during an animal examination session.

Ehsan Kazemivalipour has presented his phd thesis titled ” Innovative Designs of RF Transmit Array Coils and RF Heating Analysis of Patients with Implanted DBS ”   Abstract A safe and efficient MRI test would rely on informed specification, design, implementation, assessment, and application of appropriately selected radiofrequency (RF) coils. Towards these goals, this dissertation comprises three contributions to novel RF transmit array (TxArray) coil design techniques and two contributions to RF heating reduction of deep brain stimulation (DBS) implants in RF transmit coils. TxArray coils with multiple transmit elements provide the additional degrees of freedom that can be used to enhance field uniformity, accelerate acquisition time, enable RF shimming while intending to mitigate specific absorption rate (SAR) hotspots, and increase power efficiency. How a TxArray coil is designed can have a significant impact on its gain from parallel transmission technology. Thus, the first contribution of this dissertation is on the eigenmode analysis of the scattering matrix for the design of TxArray coils to obtain their efficient operation modes and achieve an efficient RF shimming in terms of power consumption. The algorithm is tested for the design of four 3T TxArray coils with 8 to 32 channels, and it is shown that it can enlarge the dimension of the excitation space by up to 50% compared with the commonly used design techniques. The next contribution is to establish a fast fine-tuning procedure to precisely design an imperfectly manufactured TxArray coil using its corresponding equivalent circuit model. By fitting the measured scattering parameters to a lumped circuit model, all inductances/resistances of an 8-channel 3T TxArray coil are estimated. The manufactured coil is then appropriately tuned only in a single iteration. As another contribution, a theoretical coil size optimization is introduced to minimize the magnetic coupling between non-adjacent transmit channels of a TxArray coil. By calculating all self/mutual-inductances of a 12-channel 3T TxArray coil and minimizing mutual-inductances, its sizes are determined. The finite element simulations are performed to demonstrate the feasibility of this approach. One of the safety considerations of RF transmit coils is the localized SAR amplification due to the interaction of metallic implants with the coil’s electric fields. Therefore, the fourth contribution is on evaluating SAR mitigation performance at tips of patient-derived realistic DBS implants using a 3T patient-adjustable transmit coil, which uses a mechanically rotating linearly polarized birdcage resonator. The reconfigurable coil system decreases the SAR on average by 83% for unilateral leads and by 59% for bilateral leads in comparison to a conventional quadrature birdcage coil. In the final study, the local SAR amplification surrounding the tips of a large cohort of DBS implants with realistic lead trajectories in a commercially available vertical open-bore 1.2T coil and a standard horizontal closed-bore 1.5T birdcage coil is presented. On average, SAR is decreased by 31-fold in the 1.2T vertical coil compared to the 1.5T horizontal coil. Overall, this dissertation proposes innovative approaches for designing TxArray coils and heating assessment and SAR reduction of DBS patients, which mainly contribute to improving the performance of RF transmit coils in terms of power efficiency and patient safety.  

Cemre Ariyurek, Bilal Tasdelen, Yusuf Ziya İder and Ergin Atalar have published an article titled ”SNR Weighting for Shear Wave Speed Reconstruction in Tomoelastography”  

Abstract

Bilal Tasdelen has presented his master’s thesis titled “Dynamic Decoupling and Noise Analysis for Simultaneous Transmission and Reception Imaging.” Abstract: In simultaneous transmission and reception (STAR) MRI, along with the coupling of the excitation pulse to the received signal, noise, and undesired distortions (spurs) coming from the transmit chain also leak into the acquired signal and degrade image quality. The properties of this coupled noise and its relationship with the transmit amplifier gain, transmit chain noise density, isolation performance, and imaging bandwidth are analyzed. The importance of achieving high isolation and careful selection of the corresponding parameters are demonstrated. A cancellation algorithm, together with a vector modulator, is used for transmit-receive isolation. With higher isolation, coupled transmit noise can be reduced to the point that the dominant noise source becomes acquisition noise, as in the case for pulsed MRI. Amplifiers with different gain and noise properties are used in the experiments to verify the derived noise-transmit parameter relation. With the proposed technique, more than 80 dB isolation in the analog domain is achieved. The leakage noise and the spurs coupled from the transmit chain are reduced. It is shown that the transmit gain plays the most critical role in determining sufficient isolation, whereas the amplifier noise figure does not contribute as much. Additionally, the active cancellation technique mentioned above is adapted to Magnetic Particle Imaging (MPI) for active cancellation of the direct-feedthrough. A significant increase of up to 40~dB in detection sensitivity at the fundamental harmonic on an in-house Arbitrary Waveform Relaxometer (AWR) is demonstrated.   To watch the presentation, please visit our youtube channel: https://www.youtube.com/watch?v=3zHAllZAHp4 

Phd. Student in Deep Learning for Medical Images Dr. İlkay Öksüz oksuzilkay@gmail.com Institute We offer a funded PhD. scholarships on Medical Image Acquisition and Reconstruction at the National Magnetic Resonance Center. The position will be based in Bilkent University National Magnetic Resonance Research Center (UMRAM) under supervision of Prof. Dr. Tolga Çukur. The position holder will be in close collaboration with Dr. İlkay Öksüz and Istanbul Technical University. Medical Image Analysis Several recent advances have led to more efficient ways in which MRI can be reconstructed. The most prominent example of these is compressed sensing MRI, which allows the reconstruction of MRI from under-sampled k-space data. The reconstruction of the MRI requires solving a non-linear optimization problem. For medical image reconstruction, machine learning can play a key role. The project aims to exploit recent advances in machine learning, in particular in the area of representation learning to learn representations and priors directly from raw data that are optimal for recovery of images (or even for the reconstruction of clinically useful information). The key tasks for the project are: 1. Acquisition of raw cardiac MR data 2. Reconstruction of cardiac MRI from under-sampled k-space data. 3. Development of deep learning based reconstruction algorithms leveraging temporal dependencies in cardiac MRI Funding & Details PhD positions are fully funded (4500TL/month) by The Scientific and Technological Research Council of Turkey (TÜBİTAK). The prospective students will be able to attend to prestigious international conferences and spend some time in top international institutes. The candidates must be enrolled in a graduate program in Turkey and can start to work immediately. We encourage applications from underrepresented groups. Required Skills We are looking for highly motivated students with an academic background in Physics, Computer Science or Engineering. The following skills are required: • Experience with Python and deep learning libraries (e.g. Pytorch, Tensorflow or Keras). • Motivation in machine learning and computer vision problems/algorithms. • Enthusiasm to work on clinical challenges and knowledge on MR Physics. • Good academic writing skills and English communication skills.   How to Apply Please send an email to oksuzilkay@gmail.com by attaching your CV, transcript, and a brief description explaining why you want to be considered (max 1 page).

Prolonged exposure to a certain size stimulus alters the perceived size of a subsequently presented stimulus at the same location. How the rest of the visual space is affected by this size adaptation, however, has not been systematically studied before. In this study, Altan & Boyaci tested size adaptation at the adapter location as well as the rest of the visual space. Their results showed that the perceived sizes of target stimuli were affected by the adapter, not only at the adapter location but also at other locations. These findings demonstrate that size adaptation causes widespread distortion of the visual space and alters perceived size. Altan & Boyaci discuss possible computational models that may underpin the perceptual effect in their article.  

Abstract

 

Hussain A Jaber, Ilyas Çankaya, Hadeel K Aljobouri, Orhan M Koçak and Oktay Algin have published a new article titled ”Optimal Model-Free Approach Based on MDL and CHL for Active Brain Identification in fMRI Data Analysis”. Abstract Background: Cluster analysis is a robust tool for exploring the underlining structures in data and grouping them with similar objects. In the researches of functional magnetic resonance imaging (fMRI), clustering approaches attempt to classify voxels depending on their time-course signals into a similar hemodynamic response over time.   Objective: In this work, a novel unsupervised learning approach is proposed that relies on using Enhanced Neural Gas (ENG) algorithm in fMRI data for comparison with Neural Gas (NG) method, which has yet to be utilized for that aim. The ENG algorithm depends on the network structure of the NG and concentrates on an efficacious prototype-based clustering approach.   Methods: The comparison outcomes on real auditory fMRI data show that ENG outperforms the NG and statistical parametric mapping (SPM) methods due to its insensitivity to the ordering of input data sequence, various initializations for selecting a set of neurons, and the existence of extreme values (outliers). The findings also prove its capability to discover the exact and real values of a cluster number effectively.   Results: Four validation indices are applied to evaluate the performance of the proposed ENG method with fMRI and compare it with a clustering approach (NG algorithm) and model-based data analysis (SPM). These validation indices include the Jaccard Coefficient (JC), Receiver Operating Characteristic (ROC), Minimum Description Length (MDL) value, and Minimum Square Error (MSE).   Conclusion: The ENG technique can tackle all shortcomings of NG application with fMRI data, identify the active area of the human brain effectively, and determine the locations of the cluster center based on the MDL value during the process of network learning.   Keywords: Enhanced Neural Gas (ENG); fMRI Clustering Technique; Minimum Description Length (MDL); Neural Gas (NG); Prototype-based Clustering (PBC).   https://pubmed.ncbi.nlm.nih.gov/32748753/

Ecrin Yagiz, Ahmet Rahmetullah Cagil, and Emine Ulku Saritas have published an article titled “Non-ideal Selection Field Induced Artifacts in X-Space MPI” in International Journal on Magnetic Particle Imaging. Magnetic Particle Imaging (MPI) is an emerging medical imaging modality that images the spatial distribution of superparamagnetic iron oxide (SPIO) nanoparticles using their nonlinear response to applied magnetic fields. This work demonstrates that unaccounted non-linearity of the selection field in MPI causes warping in the image reconstructed with a basic x-space approach. Unwarping algorithms can be applied to effectively address this issue, once the displacement map acting on the reconstructed image is determined. The unwarped image accurately represents the locations of nanoparticles, albeit with a resolution loss in regions away from the center of the scanner due to the degradation in selection field gradients.   Asbtract In magnetic particle imaging (MPI), the selection field deviates from its ideal linearity in regions away from the center of the scanner. This work demonstrates that unaccounted non-linearity of the selection field causes warping in the image reconstructed with a basic x-space approach. We also show that unwarping algorithms can be applied to effectively address this issue, once the displacement map acting on the reconstructed image is determined. The unwarped image accurately represents the locations of nanoparticles, albeit with a resolution loss in regions away from the center of the scanner due to the degradation in selection field gradients.