News

Semih Kurt, Yavuz Muslu and Emine Ulku Saritas have published an article titled ” Partial FOV Center Imaging (PCI): A Robust X-Space Image Reconstruction for Magnetic Particle Imaging” in IEEE Transactions on Medical 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. In this work, a robust x-space image reconstruction technique called Partial FOV Center Imaging (PCI) is proposed, with substantially simplified processing steps. Extensive simulations as well as imaging experiments on the in-house MPI scanner at UMRAM show that PCI offers a trade-off between noise robustness and interference robustness, outperforming standard x-space reconstruction in terms of both robustness against non-ideal signal conditions and image quality.

Abstract:
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. In standard x-space approach to MPI, the image is reconstructed by gridding the speed-compensated nanoparticle signal to the instantaneous position of the field free point (FFP). However, due to safety limits on the drive field, the field-of-view (FOV) needs to be covered by multiple relatively small partial field-of-views (pFOVs). The image of the entire FOV is then pieced together from individually processed pFOVs. These processing steps can be sensitive to non-ideal signal conditions such as harmonic interference, noise, and relaxation effects. In this work, we propose a robust x-space reconstruction technique, Partial FOV Center Imaging (PCI), with substantially simplified pFOV processing. PCI first forms a raw image of the entire FOV by mapping MPI signal directly to pFOV center locations. The corresponding MPI image is then obtained by deconvolving this raw image by a compact kernel, whose fully-known shape solely depends on the pFOV size.We analyze the performance of the proposed reconstruction via extensive simulations, as well as imaging experiments on our in-house FFP MPI scanner. The results show that PCI offers a tradeoff between noise robustness and interference robustness, outperforming standard x-space reconstruction in terms of both robustness against non-ideal signal conditions and image quality.

https://ieeexplore.ieee.org/document/9095326

Our UMRAM researcher Dr. Dilan Çelebi-Birand‘s article, titled “Dietary and Pharmacological Interventions That Inhibit Mammalian Target of Rapamycin Activity Alter the Brain Expression Levels of Neurogenic and Glial Markers in an Age-and Treatment-Dependent Manner” has been published.

Abstract
Intermittent fasting (IF) and its mimetic, rapamycin extend lifespan and healthspan through mechanisms that are not fully understood. We investigated different short-term durations of IF and rapamycin on cellular and molecular changes in the brains of young (6–10 months) and old (26–31 months) zebrafish. Interestingly, our results showed that IF significantly lowered glucose levels while increasing DCAMKL1 in both young and old animals. This proliferative effect of IF was supported by the upregulation of foxm1 transcript in old animals. Rapamycin did not change glucose levels in young and old animals but had differential effects depending on age. In young zebrafish, proliferating cell nuclear antigen and the LC3-II/LC3-I ratio was decreased, whereas glial fibrillary acidic protein and gephyrin were decreased in old animals. The changes in proliferative markers and a marker of autophagic flux suggest an age-dependent interplay between autophagy and cell proliferation. Additionally, changes in glia and inhibitory tone suggest a suppressive effect on neuroinflammation but may push the brain toward a more excitable state. Mammalian target of rapamycin (mTOR) activity in the brain following the IF and rapamycin treatment was differentially regulated by age. Interestingly, rapamycin inhibited mTOR more potently in young animals than IF. Principal component analysis supported our conclusion that the regulatory effects of IF and rapamycin were age-specific, since we observed different patterns in the expression levels and clustering of young and old animals. Taken together, our results suggest that even a short-term duration of IF and rapamycin have significant effects in the brain at young and old ages, and that these are age and treatment dependent.

https://www.liebertpub.com/doi/10.1089/rej.2019.2297

Bilkent University hosted the 7th International Symposium on Brain and Cognitive Science (ISBCS 2020) on 31st May 2020 with the contribution of Psychology and Philosophy departments as well as the Neuroscience program. The conference was planned to take place on campus in the Spring semester but due to COVID-19 it was transformed into a virtual conference on twitter. 

UMRAM faculty members Burcu Ayşen Ürgen, Hüseyin Boyacı, Hulusi Kafalıgönül and Michelle Adams as well as Simon Wigley from the Philosophy department at Bilkent were involved in the organization of the conference. 

There were 4 invited speakers from the US and Europe, whose pre-recorded video talks were followed by a live Q&A session on twitter. There were also 32 video posters. Poster presenters presented their work as 5-min pre-recorded videos, and got instant feedback on twitter from the symposium attendants. 

All the videos of the symposium can be accessed from the website:

http://isbcs2020.bilkent.edu.tr/program.html

All the discussions in the virtual symposium can be viewed on twitter: 

https://twitter.com/isbcs2020

In line with the Bilkent University’s decision on transition to new working conditions, we would like to announce the following principles about the work order at UMRAM starting from 01 June 2020.

1) MR scanner and other laboratories for human experiments shall be available. Specific procedures about the usage of such facilities shall be announced separately. 

2) Personnel is expected to resume regular working hours at offices. Individuals who have chronic diseases stopping them to resume work at offices should get in touch with UMRAM management.   

3) It is expected that everybody obeys rules on wearing masks and keeping social distance.  Masks will be available at UMRAM.

4) For other services and topics, the university’s announcements should be followed.

In accordance with the measures taken by the state and university due to Covid19 epidemic, in UMRAM:

1)      Our employees  are encouraged to work fom home where possible.  In this context, the number of researchers who physically present in UMRAM has been  significantly reduced.
2)      All experimental MR Imagings  and animal experiments has been cancelled.
3)      Physical meetings are  held in the form of video conferences .
4)      There are hand antiseptics at the common areas in the center.
5)      To comply with the social distancing rule and the use of  masks at the center is mandatory.

Salman Ul Hassan Dar, Muzaffer Özbey, Ahmet Burak Çatlı, and Tolga Çukur published an article entitled “A Transfer‐Learning Approach for Accelerated MRI Using Deep Neural Networks” in Magnetic Resonance in Medicine at UMRAM. 

Abstract 

Purpose 

Neural networks have received recent interest for reconstruction of undersampled MR acquisitions. Ideally, network performance should be optimized by drawing the training and testing data from the same domain. In practice, however, large datasets comprising hundreds of subjects scanned under a common protocol are rare. The goal of this study is to introduce a transfer‐learning approach to address the problem of data scarcity in training deep networks for accelerated MRI. 

Methods 

Neural networks were trained on thousands (upto 4 thousand) of samples from public datasets of either natural images or brain MR images. The networks were then fine‐tuned using only tens of brain MR images in a distinct testing domain. Domain‐transferred networks were compared to networks trained directly in the testing domain. Network performance was evaluated for varying acceleration factors (4‐10), number of training samples (0.5‐4k), and number of fine‐tuning samples (0‐100). 

Results 

The proposed approach achieves successful domain transfer between MR images acquired with different contrasts (T1‐ and T2‐weighted images) and between natural and MR images (ImageNet and T1‐ or T2‐weighted images). Networks obtained via transfer learning using only tens of images in the testing domain achieve nearly identical performance to networks trained directly in the testing domain using thousands (upto 4 thousand) of images. 

Conclusion 

The proposed approach might facilitate the use of neural networks for MRI reconstruction without the need for collection of extensive imaging datasets. 

Former UMRAM student, Ali Çağlar Özen has authored an MRM article in collaboration with Ergin Atalar on increasing the safety profile of active catheters for possible use in MR-guided cardiovascular interventions. Dr. Çağlar is currently working at the University of Freiburg. The other authors of the article are from the same university. The title of the work is “MR safety watchdog for active catheters: Wireless impedance control with real‐time feedback.”

Abstract

UMRAM Users meeting was held with all users from different areas. Also new year celebration was held.

National Magnetic Resonance Research Center (UMRAM) of Bilkent University is organizing “UMRAM Users Meeting” to bring together the interdisciplinary group of researchers that utilize the infrastructure of UMRAM for their research projects. Established in 2009 at Bilkent Cyberpark, UMRAM has the mission to promote, facilitate, and conduct research on magnetic resonance imaging (MRI) and related fields. UMRAM facilities include a Siemens 3T MAGNETOM Trio A Tim System MRI Scanner and Scimedix SM160 1.5T MRI scanner, which are solely dedicated to research. UMRAM also houses animal research, electronics, and psychophysics laboratories.

The program will be held on 13 December 2019, Friday from 09:00 to 17:00 and end with an early New Year’s celebration & dinner.

Also a poster session will be held between after lunch break.