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1.  Development of novel and low-cost readout electronics for large FOV gamma camera detector

Aram Radnia, Amirhossein Alikhani, Behnoosh Teimourian, Mahyar Youser Nejad, Mohammad Hossein Farahani, Fakhereh Pashaei, Arman Rahmim, Mohammad Reza Ay
Peer-reviewed Journal Publication
Physica Medica,2024,V 121

2.  The effect of harmonization on the variability of PET radiomic features extracted using various segmentation methods

Seyyed Ali Hosseini, Isaac Shiri, Pardis Ghaffarian, Ghasem Hajianfar, Atlas Haddadi Avval, Milad Seyfi, Stijn Servaes, Pedro Rosa-Neto, Habib Zaidi, Mohammad Reza Ay
Peer-reviewed Journal Publication
Annals of Nuclear Medicine,2024,P 1-15

3.  Automated deep identification of radiopharmaceutical type and body region from PET images

Ali Ghafari, Peyman Sheikhzadeh, Negisa Seyyedi, Mehrshad Abbasi, Shadab Ahamed, Mohammad Reza Ay, Arman Rahmim
Peer-reviewed Journal Publication
Iranian Journal of Nuclear Medicine,2024

4.  Deep learning-based partial volume correction in standard and low-dose positron emission tomography-computed tomography imaging

Mohammad-Saber Azimi, Alireza Kamali-Asl, Mohammad-Reza Ay, Navid Zeraatkar, Mahboubeh-Sadat Hosseini, Amirhossein Sanaat, Habibollah Dadgar, Hossein Arabi
Peer-reviewed Journal Publication
Quantitative Imaging in Medicine and Surgery,2024,V 14, P 2146

5.  Attention-based deep neural network for partial volume correction in brain 18F-FDG PET imaging

MohammadSaber Azimi, Alireza Kamali-Asl, Mohammad-Reza Ay, Navid Zeraatkar, Mahboube-Sadat Hosseini, Amirhossein Sanaat, Hossein Arabi
Peer-reviewed Journal Publication
Physica Medica, 2024,V 119

6.  Design and performance evaluation of partial geometry configurations of total-body PET: A Monte Carlo study

Hadi Rezaei, Peyman Sheikhzadeh, Pardis Ghafarian, Mohammad Reza Ay
Peer-reviewed Journal Publication
Iranian Journal of Nuclear Medicine,2024,V 32,P 52-59

7.  Multimodality radiomics prediction of radiotherapy-induced the early proctitis and cystitis in rectal cancer patients: A machine learning study

Samira Abbaspour, Maedeh Barahman, Hamid Abdollahi, Hossein Arabalibeik, Ghasem Hajianfar, Mohammadreza Babaei, Hamed Iraji, Mohammadreza Barzegartahamtan, Mohammadreza Ay, Seied Rabi Mahdavi
Peer-reviewed Journal Publication
Biomedical Physics & Engineering Express,2023

8.  Impact of random and scattered coincidences from outside of field of view on positron emission tomography/computed tomography imaging with different reconstruction protocols

Mahak Osouli Alamdari, Pardis Ghafarian, Arman Rahmim, Mehrdad Bakhshayesh-Karam, Mohammad Reza Ay
Peer-reviewed Journal Publication
Nuclear Science and Techniques,2023, V34,P 1-13

9.  Accurate modeling and performance evaluation of a total‐body pet scanner using Monte Carlo simulations

Hadi Rezaei, Peyman Sheikhzadeh, Pardis Ghafarian, Habib Zaidi, Mohammad Reza Ay
Peer-reviewed Journal Publication
Medical Physics,2023, V 50,P6815-6827

10.  The effects of various penalty parameter values in Q.Clear algorithm for rectal cancer detection on 18F‑FDG images using a BGO‑based PET/CT scanner: a phantom and clinical study

Fatemeh Sadeghi, Peyman Sheikhzadeh* , Saeed Farzanehfar , Pardis Ghafarian*, Yalda Moafpurian and Mohammadreza Ay
Peer-reviewed Journal Publication
EJNMMI physics,2023,V 10,P 63

11.  List-mode quantitative joint reconstruction of activity and attenuation maps in Time-of-Flight PET

Hamidreza Hemmati, Alireza Kamali-Asl, Pardis Ghafarian, Arman Rahmim, Habib Zaidi, Mohammad Reza Ay
Peer-reviewed Journal Publication
Journal of Instrumentation,V 18,P P09041

12.  FEASIBILITY OF [64CU] CU-TRASTUZUMAB PET/CT IMAGING IN BREAST CANCER: A SYSTEMATIC REVIEW

Ali Abdulhasan Kadhim, Peyman Sheikhzadeh, Mehrshad Abbasi, Nasim Vahidfar, Saeed Afshar, Mohsen Bakhshi Kashi, Negisa Seyyedi, Mohammad Reza Ay
Peer-reviewed Journal Publication
Journal of Population Therapeutics and Clinical Pharmacology, 2023,V 30, P 2375-2385

13.  Phantom and clinical evaluation of Block Sequential Regularized Expectation Maximization (BSREM) Reconstruction Algorithm in 68Ga-PSMA PET/CT Studies

Fatemeh Sadeghi, Peyman Sheikhzadeh, Nima Kasraie, Saeed Farzanehfar, Mehrshad Abbasi, Yalda Salehi, Mohammad Reza Ay
Peer-reviewed Journal Publication
Physical and Engineering Sciences in Medicine, V 3,P 1297-1308

14.  Evaluation of deep-learning based partial volume correction of PET images without the use of anatomical information

Mohammad-Saber Azimi, Alireza Kamali-Asl, Mohammad-Reza Ay, Mahboube Sadat Hosseini, Fatemeh Khorshidi, Yalda Moafpourian, Hossein ARABI, Arman Rahmim, Habib Zaidi
Peer-reviewed Journal Publication
Journal of Nuclear Medicine, V 64, P971-P971

15.  Reproducibility of radiomics features in partial volume correction of PET images

Mohammad-Saber Azimi, Alireza Kamali-Asl, Mohammad-Reza Ay, Mahboube Sadat Hosseini, Fatemeh Khorshidi, Hossein ARABI, Arman Rahmim, Habib Zaidi
Peer-reviewed Journal Publication
Journal of Nuclear Medicine,V64,P994-P994

16.  Evaluation and optimization of geometry parameters of GAGG scintillator-based Compton Camera for medical imaging by Monte Carlo simulation

Hajar Zarei, S Razaghi, Y Nagao, M Itoh, M Yamaguchi, N Kawachi, MR Ay, H Watabe
Peer-reviewed Journal Publication
Journal of Instrumentation,2023,V18, P01035

17.  Role of Lesion-to-Background Activity Ratio and Background Activity in Optimization of Reconstruction Protocols for FDG PET/CT Images of Overweight Patients: A Phantom Study

Samira Rezvani, Pardis Ghafarian, Mehrdad Bakhshayesh Karam, Mohammadreza Ay
Peer-reviewed Journal Publication
Iranian Journal of Radiology,2023,

18.  Realizing 32-time Scan Duration Reduction of 18F-FDG PET Using a Cycle-GAN and Image Augmentation

Ali Ghafari, Peyman Sheikhzadeh, Negisa Seyyedi, Mehrshad Abbasi, Mohammad Reza Ay
Peer-reviewed Journal Publication
Frontiers in Biomedical Technologies

19.  Reducing scan time using time-of-flight protocol in clinical [18F] FDG-PET/CT imaging: A feasibility study

Roya Sharifpour, Pardis Ghafarian, Mehrdad Bakhshayesh-Karam, Carlos F Uribe, Arman Rahmim, Mohammad Reza Ay
Peer-reviewed Journal Publication
Iranian Journal of Nuclear Medicine,2022,P 1-16

20.  Impact of Various Image Reconstruction Methods on Joint Compensation of Respiratory Motion and Partial Volume Effects in Whole-Body 18F-FDG PET/CT Imaging: Patients with Non-Small Cell Lung Cancer

Pardis Ghafarian, Sahar Rezaei, Esmaeil Gharepapagh, Saeid Sarkar, Mohammad Reza Ay
Peer-reviewed Journal Publication
Iran South Med J 2022, 25(4): 355-370

21.  Endorectal ultrasound radiomics in locally advanced rectal cancer patients: despeckling and radiotherapy response prediction using machine learning

Samira Abbaspour, Hamid Abdollahi, Hossein Arabalibeik, Maedeh Barahman, Amir Mohammad Arefpour, Pedram Fadavi, Mohammadreza Ay & Seied Rabi Mahdavi
Peer-reviewed Journal Publication
Nuclear Medicine Communications,2022,V 43,P 1004-1014

22.  Generation of 18F-FDG PET standard scan images from short scans using cycle-consistent generative adversarial network

Ali Ghafari, Peyman Sheikhzadeh, Negisa Seyyedi, Mehrshad Abbasi, Saeed Farzenefar, Fereshteh Yousefirizi, Mohammadreza Ay, Arman Rahmim
Peer-reviewed Journal Publication
Physics in Medicine & Biology,2022,P 355-370

23.  Deep Learning Based Missing Information Recovery in Partial Ring Total Body PET Scanner

H Rezaei, P Sheikhzadeh, P Ghafarian, I Shiri, M Ay
Proceeding and Conference Record
EUROPEAN JOURNAL OF NUCLEAR MEDICINE AND MOLECULAR IMAGING,2022,V49,S78-S79

24.  Development of Reconstruction Algorithm for High Resolution microPET Scanner Using Siddon-based System Matrix

S Hariri Tabrizi, B Teimourian, M Farahani, M Ay
Proceeding and Conference Record
EUROPEAN JOURNAL OF NUCLEAR MEDICINE AND MOLECULAR IMAGING,2022,V49, S426-S426

25.  High Resolution PET Detector Design Using SiPM Array

A Radnia, M Farahani, M Ay
Proceeding and Conference Record
EUROPEAN JOURNAL OF NUCLEAR MEDICINE AND MOLECULAR IMAGING,2022,V49,S450-S450

26.  Impact of Different Crystal Material on Performance Characteristics of Long Axial Field-Of-View PET Scanner: A Monte Carlo Simulation Study

H Rezaei, M Ay
Proceeding and Conference Record
EUROPEAN JOURNAL OF NUCLEAR MEDICINE AND MOLECULAR IMAGING,2022,V49,S79

27.  Optimization of Time Coincidence Window and Energy Window for Dedicated Brain PET: A Simulation Study

T Zare, P Sheikhzadeh, A Rahmim, B Teimourian Fard, P Ghafarian, M Ay
Proceeding and Conference Record
EUROPEAN JOURNAL OF NUCLEAR MEDICINE AND MOLECULAR IMAGING,2022,V49,S595

28.  Potential advantages of FDG‐PET radiomic feature map for target volume delineation in lung cancer radiotherapy

Zahra Falahatpour, Parham Geramifar, Seyed Rabie Mahdavi, Hamid Abdollahi, Yazdan Salimi, Alireza Nikoofar, Mohammad Reza Ay
Peer-reviewed Journal Publication
Journal of Applied Clinical Medical Physics,2022,V23

29.  The impact of Different Reconstruction Parameters along with TOF and PSF in PET/CT Imaging: Patient with Normal and High BMI

S Rezvani, P Ghafarian, M Ay
Proceeding and Conference Record
EUROPEAN JOURNAL OF NUCLEAR MEDICINE AND MOLECULAR IMAGING,2022,V49,S594

30.  Comparison of The Performance of Denoising Filters in Improving The Quality of Low-Dose Brain PET Images With Two Dose Levels of 5% and 10%

Mohammad-Saber Azimi, Alireza Kamali-asl, Mohammad-Reza Ay, Hossein Arabi
Peer-reviewed Journal Publication
medical journal of mashhad university of medical sciences,2022, Vol 65

31.  Deep Learning-Based Partial Volume Correction in Standard and Low-Dose PET-CT Imaging

Mohammad-Saber Azimi, Alireza Kamali-Asl, Mohammad-Reza Ay, Navid Zeraatkar, Hossein Arabi
Peer-reviewed Journal Publication
arXiv preprint arXiv:2207.02553

32.  Comparative assessment of attention-based deep learning and non-local mean filtering for joint noise reduction and partial volume correction in low-dose PET imaging

Mohammad-Saber Azimi, Alireza Kamali-Asl, Mohammad-Reza Ay, Navid Zeraatkar, Mahboube Sadat Hosseini, Hossein ARABI, Habib Zaidi
Peer-reviewed Journal Publication
Journal of Nuclear Medicine, 2022, Vol 63, P 2729-2729

33.  Harmonization based on quantitative analysis of standardized uptake value variations across PET/CT scanners: a multicenter phantom study

Abbas Monsef, Mohammad Reza Ay, Peyman Sheikhzadeh, Parham Geramifar, Arman Rahmim, Pardis Ghafarian
Peer-reviewed Journal Publication
Nuclear Medicine Communications,2022,V43, P1004-1014

34.  A deep learning method for high-quality ultra-fast CT image reconstruction from sparsely sampled projections

Hamidreza Khodajou-Chokami, Seyed Abolfazl Hosseini, Mohammad Reza Ay
Peer-reviewed Journal Publication
Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment,2022,Vol 1029

35.  Synergistic impact of motion and acquisition/reconstruction parameters on 18F-FDG PET radiomic features in non-small cell lung cancer: phantom and clinical studies

Seyyed Ali Hosseini,Isaac Shiri,Ghasem Hajianfar,Bahador Bahadorzade,Pardis Ghafarian,Habib Zaidi,Mohammad Reza Ay
Peer-reviewed Journal Publication
Medical Physics,2022

36.  Necessity of Development and Manufacturing of Dedicated Brain PET Scanners

Peyman Sheikhzadeh, Mohammadreza Ay
Peer-reviewed Journal Publication
Frontiers in Biomedical Technologies,2022,V9, p74-75

37.  PARS-NET: a novel deep learning framework using parallel residual conventional neural networks for sparse-view CT reconstruction

H Khodajou-Chokami, SA Hosseini, MR Ay
Peer-reviewed Journal Publication
Journal of Instrumentation,2022, Vol 17

38.  A novel approach for extracting functional brain networks involved in mesial temporal lobe epilepsy based on self organizing maps

Alireza Fallahi, Mohammad Pooyan, Jafar Mehvari Habibabadi, Seyed Sohrab Hashemi-Fesharaki, Narges Hoseini Tabatabaei, Mohammadreza Ay, Mohammad-Reza Nazem-Zadeh
Peer-reviewed Journal Publication
Informatics in Medicine Unlocked,2022, Vol 29, P 100876

39.  Statistical analysis of COVID-19 infection severity in lung lobes from chest CT

Mehdi Yousefzadeh, Mozhdeh Zolghadri, Masoud Hasanpour, Fatemeh Salimi, Ramezan Jafari, Mehran Vaziri Bozorg, Sara Haseli, Abolfazl Mahmoudi Aqeel Abadi, Shahrokh Naseri, Mohammadreza Ay, Mohammad-Reza Nazem-Zadeh
Peer-reviewed Journal Publication
Informatics in Medicine Unlocked,2022,P 100935,

40.  Leveraging Deep Neural Networks to Improve Numerical and Perceptual Image Quality in, Low-dose Preclinical PET Imaging

Mahsa Amirrashedi, Saeed Sarkar, Hojjat Mamizadeh, Hossein Ghadiri, Pardis Ghafarian, Habib Zaidi, Mohammad Reza Ay
Peer-reviewed Journal Publication
Computerized Medical Imaging and Graphics,2021,P 102010

41.  The Impact of Preprocessing on the PET-CT Radiomics Features in Non-small Cell Lung Cancer

Seyyed Ali Hosseini, Isaac Shiri, Ghasem Hajianfar, Pardis Ghafarian, Mehrdad Bakhshayesh Karam, Mohammad Reza Ay
Peer-reviewed Journal Publication
Frontiers in Biomedical Technologies,2021,V 8

42.  Accurate Monte Carlo Modeling and Performance Evaluation of a Total-body PET Scanner

Hadi Rezaei, Peyman Sheikhzadeh, Pardis Ghafarian, Habib Zaidi, Mohammad Reza Ay
Proceeding and Conference Record
2021 IEEE Nuclear Science Symposium and Medical Imaging Conference (NSS/MIC),P 1-3

43.  Temporal and extratemporal atrophic manifestation of temporal lobe epilepsy using voxel-based morphometry and corticometry: clinical application in lateralization of epileptogenic zone

Majdi Jber, Jafar Mehvari Habibabadi, Roya Sharifpour, Hengameh Marzbani, Masoud Hassanpour, Milad Seyfi, Neda Mohammadi Mobarakeh, Ahmedreza Keihani, Seyed Sohrab Hashemi-Fesharaki, Mohammadreza Ay, Mohammad-Reza Nazem-Zadeh
Peer-reviewed Journal Publication
Neurological Sciences,2021,P 1-21

44.  Introducing a novel Polyvinyl chloride/Tungsten composites for shielding against gamma and X-ray radiations

Tohid Abdolahzadeh1 , Jalil Morshedian1 , Shervin Ahmadi1 , Mohammad Reza Ay2,3 , Omid Mohammadi
Peer-reviewed Journal Publication
Iranian Journal of Nuclear Medicine,2021,vol 29- p 58-64

45.  Introducing the GammaPen: All-in-One Gamma Probe for Sentinel Lymph Node Biopsy

Aram Radnia, Hamed Abdollahzadeh, Behnoosh Teimourian, Mohammad Hossein Farahani, Mohammad Reza Ay
Peer-reviewed Journal Publication
Frontiers in Biomedical Technologies,2021

46.  Dynamic functional connectivity in temporal lobe epilepsy: a graph theoretical and machine learning approach

Alireza Fallahi, Mohammad Pooyan, Nastaran Lotfi, Fatemeh Baniasad, Leili Tapak, Neda Mohammadi-Mobarakeh, Seyed Sohrab Hashemi-Fesharaki, Jafar Mehvari-Habibabadi, Mohammad Reza Ay, Mohammad-Reza Nazem-Zadeh
Peer-reviewed Journal Publication
Neurological Sciences,2021,Vol 42

47.  A Deep Neural Network To Recover Missing Data In Small Animal Pet Imaging: Comparison Between Sinogram-And Image-Domain Implementations

Mahsa Amirrashedi, Saeed Sarkar, Hossein Ghadiri, Pardis Ghafarian, Habib Zaidi, Mohammad Reza Ay
Proceeding and Conference Record
2021 IEEE 18th International Symposium on Biomedical Imaging (ISBI)

48.  Standard-dose PET reconstruction from low-dose preclinical images using an adopted all convolutional U-Net

Mahsa Amirrashedi, Saeed Sarkar, Hossein Ghadiri, Pardis Ghafarian, Mohammad Reza Ay
Proceeding and Conference Record
Medical Imaging 2021: Biomedical Applications in Molecular, Structural, and Functional Imaging

49.  Development and characterization of an all-in-one gamma probe with auto-peak detection for sentinel lymph node biopsy based on NEMA NU3-2004 standard

Aram Radnia, Hamed Abdollahzadeh, Behnoosh Teimourian, Mohammad Hossein Farahani, Mohammad Esmaeil Akbari, Habib Zaidi, Mohammad Reza Ay
Peer-reviewed Journal Publication
Annals of Nuclear Medicine,2021,Vol 35,P 1-9

50.  Advances in Preclinical PET Instrumentation

Mahsa Amirrashedi, Habib Zaidi, Mohammad Reza Ay
Peer-reviewed Journal Publication
Elsevier,2020, V4,p403-426

51.  Measurement of Radiation Exposure to Caregivers of Patients with Thyroid Diseases Treated with Iodine-131: A Review

Ali Abdulhasan Kadhim, Peyman Sheikhzadeh, Saeed Farzanefar, Shima Yavari, Majdi Mousa Jber, Mohammad Reza Ay
Peer-reviewed Journal Publication
Frontiers in Biomedical Technologies,Vol 7,P 191-199

52.  Evaluation of gamma and electron radiations impact on vitamins for onion preservation

Salar Firouzi, Abdollah Khorshidi, Jamshid Soltani-Nabipour, Seyed Mohsen Zia Barzi, Mohammad Amani, Majid Sorouri, Mohammad Reza Ay
Peer-reviewed Journal Publication
Applied Radiation and Isotopes,2020

53.  Towards quantitative small-animal imaging on hybrid PET/CT and PET/MRI systems

Mahsa Amirrashedi, Habib Zaidi, Mohammad Reza Ay
Peer-reviewed Journal Publication
Clinical and Translational Imaging,2020

54.  Radiation Dose Assessment to Family Members Taking Care of Non-Cancerous Thyroid Patients Treated with I-131 Therapy in Nuclear Medicine Department

Ali Abdulhasan Kadhim, Peyman Sheikhzadeh, Saeed Farzanefar, Shima Yavari, Mohammad Reza Ay
Peer-reviewed Journal Publication
Radiation Protection Dosimetry,2020

55.  Deep-JASC: joint attenuation and scatter correction in whole-body 18F-FDG PET using a deep residual network

Isaac Shiri, Hossein Arabi, Parham Geramifar, Ghasem Hajianfar, Pardis Ghafarian, Arman Rahmim, Mohammad Reza Ay & Habib Zaidi
Peer-reviewed Journal Publication
European Journal of Nuclear Medicine and Molecular Imaging, 2020

56.  Guidelines for TMS/tES Clinical Services and Research through the COVID-19 Pandemic

Marom Bikson, Colleen A Hanlon, Adam J Woods, Bernadette T Gillick, Leigh Charvet, Claus Lamm, Graziella Madeo, Adrienn Holczer, Jorge Almeida, Andrea Antal, Mohammad Reza Ay,
Peer-reviewed Journal Publication
Brain Stimulation, Elsevier,2020

57.  Standard SPECT myocardial perfusion estimation from half-time acquisitions using deep convolutional residual neural networks

Isaac Shiri, Kiarash AmirMozafari Sabet, Hossein Arabi, Mozhgan Pourkeshavarz, Behnoosh Teimourian, Mohammad Reza Ay, Habib Zaidi
Peer-reviewed Journal Publication
Journal of nuclear cardiology: official publication of the American Society of Nuclear Cardiology,2020

58.  Performance evaluation of developed dedicated breast PET scanner and improvement of the spatial resolution by wobbling: a Monte Carlo study.

A Emami, H Ghadiri, P Ghafarian, P Geramifar, MR Ay
Peer-reviewed Journal Publication
Japanese journal of radiology,2020,P 1-10

59.  6th Anniversary Editorial

Mahnaz Kiani Mobareke, Mohmmadreza Ay
Peer-reviewed Journal Publication
Frontiers in Biomedical Technologies,Vol 7, P 1-2

60.  Novel preclinical PET geometrical concept using a monolithic scintillator crystal offering concurrent enhancement in spatial resolution and detection sensitivity: a simulation study

Amirhossein Sanaat , HosseinArabi , MohammadReza Ay and Habib Zaidi
Peer-reviewed Journal Publication
Physics in Medicine & Biology,2020

61.  Computationally efficient system matrix calculation techniques in computed tomography iterative reconstruction

Golshan Mahmoudi, Mohammad Reza Ay, Arman Rahmim, Hossein Ghadiri
Peer-reviewed Journal Publication
Journal of Medical Signals and Sensors,2020,Vol 10, p 1-11

62.  Corrigendum to" Targeted gold nanoparticles enable molecular CT imaging of head and neck cancer: An in vivo study

Sara Khademi, Saeed Sarkar, Ali Shakeri-Zadeh, Neda Attaran, Sharmin Kharrazi, Mohammad Reza Ay, Hosein Azimian, Hossein Ghadiri
Peer-reviewed Journal Publication
The International Journal of Biochemistry & Cell Biology,2020, Vol 10,P 1

63.  Molecular imaging approaches in the diagnosis of breast cancer: A systematic review and meta-analysis

Getu Ferenji Tadesse, Parham Geramifar, Pardis Ghafarian, Eshetu Ejeta Cheka, Eyachew Misgana Tegaw, Seifu Gizaw Feyisa, Ramin Sadeghi, Mohammad Reza Ay
Peer-reviewed Journal Publication
Iranian Journal of Nuclear Medicine,2020,Vol 28, P 1-13

64.  The impact of iterative reconstruction protocol, signal‑to‑background ratio and background activity on measurement of PET spatial resolution

Sahar Rezaei1,2 · Pardis Ghafarian3,4 · Mehrdad Bakhshayesh‑Karam3,4 · Carlos F. Uribe5 · Arman Rahmim6,7 · Saeed Sarkar2 · Mohammad Reza Ay1,2
Peer-reviewed Journal Publication
Japanese Journal of Radiology ,2020,

65.  Validation and evaluation of a GATE model for MAMMI PET scanner

Azadeh Emami, Pardis Ghafarian, Hossien Ghadiri, Parham Geramifar, Mohammad Reza Ay
Peer-reviewed Journal Publication
Iranian Journal of Nuclear Medicine,2020,Vol 28, P 33-38

66.  Novel preclinical PET geometrical concept using a monolithic scintillator crystal offering concurrent enhancement in spatial resolution and detection sensitivity: a simulation …

Amirhossein Sanaat, Hossein Arabi, Mohammadreza Ay, Habib Zaidi
Peer-reviewed Journal Publication
Physics in Medicine & Biology,2019,

67.  Joint compensation of motion and partial volume effects by iterativedeconvolution incorporating wavelet-based denoising in oncologic PET/CTimaging

Sahar Rezaei,Pardis Ghafarian,Abhinav K. JhaArman Rahmim,Saeed Sarkar,Mohammad Reza Ay
Peer-reviewed Journal Publication
physica media,2019,Vol 68,P 52-60

68.  Targeted gold nanoparticles enable molecular CT imaging of head and neck cancer: an in vivo study

Sara Khademi, Saeed Sarkar, Ali Shakeri-Zadeh, Neda Attaran, Sharmin Kharrazi, Mohammad Reza Ay, Hosein Azimian, Hossein Ghadiri
Peer-reviewed Journal Publication
The international journal of biochemistry & cell biology,2018,Vol 114

69.  Sparse-view statistical image reconstruction with improved total variation regularization for X-ray micro-CT imaging

G Mahmoudi, MR Fouladi, MR Ay, A Rahmim, H Ghadiri
Peer-reviewed Journal Publication
Journal of Instrumentation, 2019, Vol 14

70.  NEMA NU‐4 2008 Performance Evaluation of Xtrim‐PET: A prototype Si PM‐based preclinical scanner

Mahsa Amirrashedi, Saeed Sarkar, Pardis Ghafarian, Reza Hashemi Shahraki, Parham Geramifar, Habib Zaidi, Mohammad Reza Ay
Peer-reviewed Journal Publication
Medical physics,2019

71.  A novel approach to automatic position calibration for pixelated crystals in gamma imaging

Salar Sajedi, Navid Zeraatkar, Sanaz Kaviani, Hadi Khanmohammadi, Saeed Sarkar, Hamid Sabet, Mohammad Reza Ay
Peer-reviewed Journal Publication
Iranian Journal of Nuclear Medicine,2019,Vol 27

72.  Dual-energy CT imaging of nasopharyngeal cancer cells using multifunctional gold nanoparticles

Hossein Ghadiri, Sara Khademi, Saeed Sarkar, Ali Shakeri-zadeh, Neda Attaran, Mohammad Reza Ay, Hosein Azimian, Razieh Solgi
Peer-reviewed Journal Publication
IET Nanobiotechnology, 2019

73.  The influence of misregistration between CT and SPECT images on the accuracy of CT-based attenuation correction of cardiac SPECT/CT imaging: Phantom and clinical studies

Leila Saleki, Pardis Ghafarian, Ahmad Bitarafan-Rajabi, Nahid Yaghoobi, Babak Fallahi, Mohammad Reza Ay
Peer-reviewed Journal Publication
Iranian Journal of Nuclear Medicine,2019,Vol 27,pp63-72

74.  Validation and evaluation of a GATE model for MAMMI PET scanner

Azadeh Emami, Pardis Ghafarian, Hossien Ghadiri, Parham Geramifar, Mohammad Reza Ay
Peer-reviewed Journal Publication
Iranian Journal of Nuclear Medicine,2019

75.  A Novel Method for Measuring the MTF of CT Scanners: A Phantom Study

Hamidreza Khodajou-Chokami, Seyed Abolfazl Hosseini, Mohammad Reza Ay, Ali Safarzadehamiri, Pardis Ghafarian, Habib Zaidi
Proceeding and Conference Record
2019 IEEE International Symposium on Medical Measurements and Applications

76.  MCNP-FBSM: Development of MCNP/MCNPX Source Model for Simulation of Multi-Slice Fan-Beam X-Ray CT Scanners

Hamidreza Khodajou-Chokami, Seyed Abolfazl Hosseini, Mohammad Reza Ay, Habib Zaidi
Proceeding and Conference Record
2019 IEEE International Symposium on Medical Measurements and Applications

77.  Direct attenuation correction of brain PET images using only emission data via a deep convolutional encoder-decoder (Deep-DAC)

Isaac Shiri, Pardis Ghafarian, Parham Geramifar, Kevin Ho-Yin Leung, Mostafa Ghelichoghli, Mehrdad Oveisi, Arman Rahmim, Mohammad Reza Ay
Peer-reviewed Journal Publication
European radiology,2019,pp1-3

78.  Development and preliminary results of Xtrim-PET, a modular cost-effective preclinical scanner

Salar Sajedi, Navid Zeraatkar, Mohsen Taheri, Sanaz Kaviani, Hadi Khanmohammadi, Saeed Sarkar, Hamid Sabet, Mohammad Reza Ay
Peer-reviewed Journal Publication
2019, Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment

79.  Deep-Fill: Deep Learning Based Sinogram Domain Gap Filling in Positron Emission Tomography

Isaac Shiri, Peyman Sheikhzadeh, Mohammad Reza Ay
Peer-reviewed Journal Publication
arXiv preprint arXiv:1906.07168

80.  Design, optimization and performance evaluation of BM-PET: A simulation study

Peyman Sheikhzadeh, Hamid Sabet, Hossein Ghadiri, Parham Geramifar, Pardis Ghafarian, Mohammad Reza Ay
Peer-reviewed Journal Publication
Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment

81.  PSFNET: ultrafast generation of PSF-modelled-like PET images using deep convolutional neural network

Isaac Shiri, Kevin Leung, Parham Geramifar, Pardis Ghafarian, Mehrdad Oveisi, Mohammad Reza Ay, Arman Rahmim
Peer-reviewed Journal Publication
Journal of Nuclear Medicine,2019,vol 60,pp 1369-1369

82.  HiResPET: high resolution PET image generation using deep convolution encoder decoder network

Isaac Shiri, Kevin Leung, Pardis Ghafarian, Parham Geramifar, Mehrdad Oveisi, Mohammad Reza Ay, Arman Rahmim
Peer-reviewed Journal Publication
Journal of Nuclear Medicine,2019,vol 60,pp 1368-1368

83.  Simultaneous Attenuation Correction and Reconstruction of PET Images Using Deep Convolutional Encoder Decoder Networks from Emission Data

Isaac Shiri, Kevin Leung, Pardis Ghafarian, Parham Geramifar, Mehrdad Oveisi, Mohammad Reza Ay, Arman Rahmim
Peer-reviewed Journal Publication
Journal of Nuclear Medicine,2019,vol 60

84.  Impact of image reconstruction methods on quantitative accuracy and variability of FDG-PET volumetric and textural measures in solid tumors

Ali Ketabi, Pardis Ghafarian, Mohammad Amin Mosleh-Shirazi, Seyed Rabi Mahdavi, Arman Rahmim, Mohammad Reza Ay
Peer-reviewed Journal Publication
European radiology,2019,vol 29,pp 2146-2156

85.  Techniques for generating attenuation map using cardiac SPECT emission data only: a systematic review

Getu Ferenji Tadesse, Parham Geramifar, Eyachew Misganew Tegaw, Mohammad Reza Ay,
Peer-reviewed Journal Publication
Annals of Nuclear Medicine ,21019,Vol 33,P 1-13

86.  Design and performance evaluation of high resolution small animal PET scanner based on monolithic crystal: a simulation study

A Sanaat, MS Zafarghandi, MR Ay
Peer-reviewed Journal Publication
Journal of Instrumentation,2019, Vol 14

87.  A full quantitative analysis of 18 MV photon beam from 2100 C/D-Varian clinical linear accelerator with and without flattening filter

SR Mahdavi, MR Ay, M Zabihzadeh, M Allahverdi, M Shahriari, M Hoseini-Ghahfarokhi
Peer-reviewed Journal Publication
International Journal of Radiation Research, 2019, Vol 17, P 137-146

88.  Design and performance evaluation of spheroid geometry for brain PET scanner using Monte Carlo modeling

Peyman Sheikhzadeh, Hossein Ghadiri, Parham Geramifar, Pardis Ghafarian, Mohammad Reza Ay
Peer-reviewed Journal Publication
Iranian Journal of Nuclear Medicine, 2019, Vol 27, P 32-37

89.  Monte Carlo-based optimization of a gamma probe system for sentinel lymph node mapping

Azadeh Nikoogoftar, Mojtaba Shamsaie, Navid Zeraatkar, Mohammad Reza Ay
Peer-reviewed Journal Publication
Iranian Journal of Nuclear Medicine,2019, Vol 27, p 8-14

90.  Resolution Recovery with Pre-Reconstruction Fourier Transforms Filtering for a High Resolution Animal SPECT System

Reza Hashemi Shahraki, Isaac Shiri, Parham Geramifar, Afshin Akbarzadeh, Amir Hossein Sanaat, Mohammad Reza Ay
Peer-reviewed Journal Publication
Frontiers in Biomedical Technologiesو2018Vol 5, P 74-80

91.  Advantages and disadvantages of removed flattening filter Linac: A Monte Carlo study on full quantitative dosimetric data of 18 MV-Varian Linac

Mansour Zabihzadeh, Seyed Rabee Mahdavi, Mohammad Reza Ay, Mojtaba Hoseini-Ghahfarokhi
Peer-reviewed Journal Publication
Iranian Journal of Medical Physics, 2018, Vol 15, P 446

92.  Conventional Voxel in Tomographic Reconstruction Based upon Plane-Integral Projections–Use It or Lose It?

Hojjat Mahani, Gholamreza Raisali, Alireza Kamali-Asl, Mohammad Reza Ay
Peer-reviewed Journal Publication
Iranian Journal of Medical Physics, 2018, Vol 15, P 269-269

93.  Conventional Voxel in Tomographic Reconstruction Based upon Plane-Integral Projections–Use It or Lose It?

Hojjat Mahani, Gholamreza Raisali, Alireza Kamali-Asl, Mohammad Reza Ay
Proceeding and Conference Record
Iranian Journal of Medical Physics,2018, V ol 15, P 261

94.  Evaluation of effect of gold nanorods and spherical gold nanoparticles of different sizes on X-ray attenuation in computed tomography

Sara Khademi, Hossein Ghadiri, Saeed Sarkar, Sharmin Kharrazi, Seyed Mohammad Amini, Ali Shakeri-Zadeh, Mohammad Reza Ay
Peer-reviewed Journal Publication
Iranian Journal of Medical Physics,2018, Vol 15, P 354

95.  Evaluation of multifunctional targeted gold nanoparticles on X-ray attenuation in nasopharyngeal cancer cells by X-ray imaging

Sara Khademi, Hossein Ghadiri, Saeed Sarkar, Ali Shakerizadeh, Neda Attaran, Sharmin Kharrazi, Mohammad Reza Ay
Peer-reviewed Journal Publication
Iranian Journal of Medical Physics, 2018, Vol 15, P 355

96.  Fast System Matrix Calculation in CT Iterative Reconstruction

Golshan Mahmoudi, Mohammad Reza Ay, Hossein Ghadiri
Peer-reviewed Journal Publication
Iranian Journal of Medical Physics, 2018, Vol 15, P 150-150

97.  Recovery of missing data in partial geometry PET scanners: Compensation in projection space vs image space

Seyedehsamaneh Shojaeilangari, C Ross Schmidtlein, Arman Rahmim, Mohammad Reza Ay
Peer-reviewed Journal Publication
Medical physics, 2018, Vol 45, P5437-5449

98.  Impact of image reconstruction methods on quantitative accuracy and variability of FDG-PET volumetric and textural measures in solid tumors

Ali Ketabi, Pardis Ghafarian, Mohammad Amin Mosleh-Shirazi, Seyed Rabi Mahdavi, Arman Rahmim, Mohammad Reza Ay
Peer-reviewed Journal Publication
European radiology,2018,pp1-11

99.  F-18-PSMA vs. Ga-68-PSMA11; S-value Estimation in XCAT BMIs Using GATE Monte Carlo Code

M Fallahpoor, N Vahidfar, G Divband, F Kalantari, M Ay
Proceeding and Conference Record
EUROPEAN JOURNAL OF NUCLEAR MEDICINE AND MOLECULAR IMAGING,2018, Vol 45,P S737-S737

100.  Monte Carlo simulation of MAMMI PET system and performance evaluation using GATE toolkit

A Emami, H Ghadiri, P Ghafarian, P Geramifar, M Ay
Proceeding and Conference Record
EUROPEAN JOURNAL OF NUCLEAR MEDICINE AND MOLECULAR IMAGING,2018, Vol 45, P S714-S714

101.  Uncertainties in effective dose estimation for CT transmission scan in total body PET-CT imaging with Auto mA3D tube current modulation

Y Salimi, MR Deevband, P Ghafarian, MR Ay
Peer-reviewed Journal Publication
International Journal of Radiation Research, Vol 16, p 465-472

102.  Folic acid-cysteamine modified gold nanoparticle as a nanoprobe for targeted computed tomography imaging of cancer cells

Sara Khademi, Saeed Sarkar, Ali Shakeri-Zadeh, Neda Attaran, Sharmin Kharrazi, Mohammad Reza Ay, Hossein Ghadiri
Peer-reviewed Journal Publication
Materials Science and Engineering: C,2018 ,Vol.89

103.  Reconstruction/segmentation of attenuation map in TOF-PET based on mixture models

Hamidreza Hemmati, Alireza Kamali-Asl, Pardis Ghafarian, Mohammad Reza Ay
Peer-reviewed Journal Publication
Annals of nuclear medicine, 2018, Vol.26, pp 1-11

104.  Capturing Bone Signal in MRI of Pelvis, as a Large FOV Region, Using TWIST Sequence and Generating a 5-Class Attenuation Map for Prostate PET/MRI Imaging

Mehdi Shirin Shandiz, Hamid Saligheh Rad, Pardis Ghafarian, Khadijeh Yaghoubi, Mohammad Reza Ay
Peer-reviewed Journal Publication
Molecular imaging, 2018, Vol 17

105.  Concept design and Monte Carlo performance evaluation of HeadphonePET: a novel brain-dedicated PET system based on partial cylindrical detectors

P Sheikhzadeh, H Sabet, H Ghadiri, P Geramifar, P Ghafarian, MR Ay
Peer-reviewed Journal Publication
Journal of Instrumentation, 2018, Vol 13 ,P07008

106.  An alternative mathematical modeling of the scintillation camera and framework for performance analysis of gamma-ray positioning algorithms

Behnoosh Teimourian Fard, Mojtaba Shamsaei Zafarghandi, Soheil Hosseini, Hamid Sabet, Mohammad Reza Ay
Peer-reviewed Journal Publication
Iranian Journal of Nuclear Medicine, 2018, v.26, P.112-126

107.  The influence of using different reconstruction algorithms on sensitivity of quantitative 18F-FDG-PET volumetric measures to background activity variation

Ali Ketabi, Pardis Ghafarian, Mohammad Amin Mosleh-Shirazi, Seyed Rabi Mahdavi, Mohammad Reza Ay
Peer-reviewed Journal Publication
Iranian Journal of Nuclear Medicine, 2018, Vol.26, pp 87-97

108.  Mixture model based joint-MAP reconstruction of attenuation and activity maps in TOF-PET

H Hemmati, A Kamali-Asl, P Ghafarian, MR Ay
Peer-reviewed Journal Publication
Journal of Instrumentation, 2018, Vol.13

109.  Cardiac contraction motion compensation in gated myocardial perfusion SPECT: A comparative studyRobotic system for SPECT imaging

Narges Salehi, Arman Rahmim, Emad Fatemizadeh, Afshin Akbarzadeh, Mohammad Hossein Farahani, Saeed Farzanefar, Mohammad Reza Ay
Peer-reviewed Journal Publication
Physica Medica, 2018, Vol.49, pp 77-82

110.  Generic high resolution PET detector block using 12× 12 SiPM array

Salar Sajedi, Navid Zeraatkar, Mohsen Taheri, Sanaz Kaviani, Hadi Khanmohammadi, Saeed Sarkar, Hamid Sabet, Mohammad Reza Ay
Peer-reviewed Journal Publication
Biomedical Physics & Engineering Express, 2018, Vol 4

111.  A novel dual energy method for enhanced quantitative computed tomography

A Emami, H Ghadiri, A Rahmim, MR Ay
Peer-reviewed Journal Publication
Journal of Instrumentation, 2018, Vol.13

112.  Evaluation of size, morphology, concentration, and surface effect of gold nanoparticles on X-ray attenuation in computed tomography

Sara Khademi, Saeed Sarkar, Sharmin Kharrazi, Seyed Mohammad Amini, Ali Shakeri-Zadeh, Mohammad Reza Ay, Hossein Ghadiri
Peer-reviewed Journal Publication
Physica Medica, 2018, Vol 45,pp 127-133

113.  Evaluating the Impact of Various Parameters on the Gamma Index Values of 2D Diode Array in IMRT Verification

Keyvan Jabbari, Fakhereh Pashaei, Mohammad R Ay, Alireza Amouheidari, Mohammad B Tavakoli
Peer-reviewed Journal Publication
Journal of medical signals and sensors, Vol 8 , P31-38

114.  Is correction for metallic artefacts mandatory in cardiac SPECT/CT imaging in the presence of pacemaker and implantable cardioverter defibrillator leads?

Zahra Etemadi, Pardis Ghafarian, Ahmad Bitarafan-Rajabi, Hadi Malek, Mohammad Reza Ay
Peer-reviewed Journal Publication
Iranian Journal of Nuclear Medicine, 2018, Vol 26, P 35-46

115.  Quantification and Reduction of Respiratory Induced Artifact in Attenuation Correction of PET Data using Respiration Averaged CT: A Simulation and Phantom Study

Fatemeh Sadat Fatemi Nasrollahi, Pardis Ghafarian, Parham Grramifar, Mohammad Reza Ay
Peer-reviewed Journal Publication
Frontiers in Biomedical Technologies, 2017, Vol 3, pp 49-59

116.  Quantification and reduction of respiratory induced artifacts in positron emission tomography/computed tomography using the time-of-flight technique

Roya Sharifpour, Pardis Ghafarian, Arman Rahmim, Mohammad R Ay
Peer-reviewed Journal Publication
Nuclear medicine communications

117.  A Generic, Scalable, and Cost-Effective Detector Front-End Block for PET

Salar Sajedi, Navid Zeraatkar, Mohsen Taheri, Sanaz Kaviani, Hadi Khanmohammadi, Saeed Sarkar, Hamid Sabet, MR Ay
Proceeding and Conference Record
2017 IEEE Nuclear Science Symposium and Medical Imaging Conference (NSS/MIC), P 1-3

118.  Development of a Preclinical PET System Based on Pixelated LYSO Crystals and SiPM Arrays

Navid Zeraatkar, Salar Sajedi, Sanaz Kaviani, Mohsen Taheri, Hadi Khanmohammadi, Saeed Sarkar, Mohammad Reza Ay
Proceeding and Conference Record
2017 IEEE Nuclear Science Symposium and Medical Imaging Conference (NSS/MIC), P 1-3

119.  A Comparison Study on Two Novel Statistical Reconstruction Algorithms Developed for Slit-Hole Collimation Data in Small Animal SPECT Imaging

H Mahani, G Raisali, A Kamali-Asl, M Ay
Proceeding and Conference Record
EUROPEAN JOURNAL OF NUCLEAR MEDICINE AND MOLECULAR IMAGING, 2017, Vol 44, P S434-S434

120.  Cardiac contraction motion compensation in gated Myocardial Perfusion SPECT

N Salehi, M Farahani, E Fatemizadeh, S Farzanefar, M Ay
Proceeding and Conference Record
EUROPEAN JOURNAL OF NUCLEAR MEDICINE AND MOLECULAR IMAGING, 2017

121.  Design optimization of partial cylindrical PET scanner based on trapezoid-shaped block detector and monolithic crystals using Monte Carlo simulation

P Sheikhzadeh, H Ghadiri, P Geramifar, P Ghaffarian, M Ay
Proceeding and Conference Record
EUROPEAN JOURNAL OF NUCLEAR MEDICINE AND MOLECULAR IMAGING, 2017

122.  Development of low dose CT protocols with acceptable CT image quality for CTAC of PET data: Phantom Study

Z Mojabi, P Ghafarian, H Ghadiri, M Bakhshayeshkaram, M Ay
Proceeding and Conference Record
EUROPEAN JOURNAL OF NUCLEAR MEDICINE AND MOLECULAR IMAGING, 2017

123.  Evaluation of the Impact of Using TOF Technique on Metal Artifact Reduction in PET/CT Images

R Sharifpour, P Ghafarian, MR Ay
Proceeding and Conference Record
EUROPEAN JOURNAL OF NUCLEAR MEDICINE AND MOLECULAR IMAGING, 2017

124.  Grid block design based on monte carlo simulated dosimetry, the linear quadratic and Hug–Kellerer radiobiological models

Somayeh Gholami, Hassan Ali Nedaie, Francesco Longo, Mohammad Reza Ay, Sharifeh A Dini, Ali S Meigooni
Peer-reviewed Journal Publication
Journal of medical physics, 2017, Vol 42, pp 213

125.  Is the averaged SUV from several hottest voxels an alternative to SUV peak for quantification of large heterogeneous or small lesions in oncological PET imaging?

A Ketabi, P Ghafarian, S Masjoodi, MA Mosleh-Shirazi, MR Ay
Proceeding and Conference Record
EUROPEAN JOURNAL OF NUCLEAR MEDICINE AND MOLECULAR IMAGING, 2017

126.  Monte Carlo Based Performance estimation of breast PET due to reduction of the ring diameter

A Emami, H Ghadiri, P Ghafarian, M Ay
Proceeding and Conference Record
EUROPEAN JOURNAL OF NUCLEAR MEDICINE AND MOLECULAR IMAGING, 2017

127.  Optimal quantitative SUV metrics over wide range of lesion sizes in advanced image reconstruction (TOF and PSF) for PET

I Shiri, P Ghafarian, S Ashrafinia, A Bitarafan-Rajabi, M Ay, A Rahmim
Proceeding and Conference Record
EUROPEAN JOURNAL OF NUCLEAR MEDICINE AND MOLECULAR IMAGING, 2017, Vol 44, P S427-S428

128.  Optimization of the crystal thickness for a monolithic LYSO animal PET detector with anger and CSE positioning method using Monte Carlo simulation

A Sanaat, M Shamsaie, B Teymorian, R Hoshemi, M Ay
Proceeding and Conference Record
EUROPEAN JOURNAL OF NUCLEAR MEDICINE AND MOLECULAR IMAGING, 2017, Vol 44, p 431-432

129.  Quantification and Reduction of respiratory induced errors in attenuation correction of PET data using respiration averaged CT: a simulation study

P Ghaffarian, F Fatemi, P Geramifar, M Ay
Proceeding and Conference Record
EUROPEAN JOURNAL OF NUCLEAR MEDICINE AND MOLECULAR IMAGING, 2017

130.  Simultaneous High-Sensitivity High-Resolution Molecular SPECT Imaging with Spinning Slit-Hole Collimator: A Monte Carlo Simulation Study

M Ay, H Mahani, G Raisali, A Kamali-Asl
Proceeding and Conference Record
EUROPEAN JOURNAL OF NUCLEAR MEDICINE AND MOLECULAR IMAGING, 2017, Vol 44, P S389-S390

131.  Sub-centimeter lesion detectability in Point-spread function (PSF) and Time of flight (TOF) reconstructed PET images

I Shiri, P Ghafarian, A Bitarafan-Rajabi, M Ay
Proceeding and Conference Record
EUROPEAN JOURNAL OF NUCLEAR MEDICINE AND MOLECULAR IMAGING, 2017, Vol 44, P S438-S439

132.  The Influence of Crystal Material and Size on the Sensitivity of Recently Developed SiPM Based Animal PET Scanner: a Monte Carlo Study

P Ghahramani, N Zeraatkar, N Vosoughi, MR Ay
Proceeding and Conference Record
EUROPEAN JOURNAL OF NUCLEAR MEDICINE AND MOLECULAR IMAGING, 2017, Vol 44, PS429-S430

133.  Volume-based assessment of different image reconstruction algorithms and thresholds for FDG-PET/CT based on dose-painting concept

P Ghafarian, A Ketabi, MA Mosleh-Shirazi, MR Ay
Proceeding and Conference Record
EUROPEAN JOURNAL OF NUCLEAR MEDICINE AND MOLECULAR IMAGING, 2017, Vol 44, P S758-S758

134.  Compton scatter tomography in TOF-PET

Hamidreza Hemmati, Alireza Kamali-Asl, Mohammadreza Ay, Pardis Ghafarian
Peer-reviewed Journal Publication
Physics in Medicine & Biology,2017, Vol 62, pp 7641

135.  Development and calibration of a new gamma camera detector using large square Photomultiplier Tubes

N Zeraatkar, S Sajedi, B Teimourian Fard, S Kaviani, A Akbarzadeh, MH Farahani, S Sarkar, MR Ay
Peer-reviewed Journal Publication
Journal of Instrumentation,2017, Vol 12

136.  Development and validation of an accurate GATE model for NeuroPET scanner

Peyman Sheikhzadeh, Hamid Sabet, Hossein Ghadiri, Parham Geramifar, Hojjat Mahani, Pardis Ghafarian, Mohammad Reza Ay
Peer-reviewed Journal Publication
Physica Medica, 2017,Vol.40, pp59-65

137.  Spinning slithole collimation for high-sensitivity small animal SPECT: Design and assessment using GATE simulation

Hojjat Mahani, Gholamreza Raisali, Alireza Kamali-Asl, Mohammad Reza Ay
Peer-reviewed Journal Publication
Physica Medica, 2017, Vol 40, pp 42-50

138.  Implementation of absolute quantification in small‐animal SPECT imaging: Phantom and animal studies

Shabnam Khorasani Gerdekoohi, Naser Vosoughi, Kaveh Tanha, Majid Assadi, Pardis Ghafarian, Arman Rahmim, Mohammad Reza Ay
Peer-reviewed Journal Publication
Journal of applied clinical medical physics, 2017, Vol 18, pp 215-223

139.  How crystal configuration affects the position detection accuracy in pixelated molecular SPECT imaging systems?

Hojjat Mahani, Gholamreza Raisali, Alireza Kamali-Asl, Mohammad Reza Ay
Peer-reviewed Journal Publication
Nuclear Science and Techniques, 2017, Vol 28, pp 47

140.  Implementation of absolute quantification in small-animal SPECT imaging: Phantom and animal studies

Shabnam Khorasani Gerdekoohi, Naser Vosoughi, Kaveh Tanha, Majid Assadi, Pardis Ghafarian, Arman Rahmim, Mohammad Reza Ay
Peer-reviewed Journal Publication
MEDICAL IMAGING, 2017, pp 1-9

141.  Evaluation of radiation exposure to staff and environment dose from [18F]-FDG in PET/CT and cyclotron center using thermoluminescent dosimetry

S Zargan, P Ghafarian, A Shabestani Monfared, AA Sharafi, M Bakhshayeshkaram, MR Ay
Peer-reviewed Journal Publication
Journal of biomedical physics & engineering, 2017,Vol 7

142.  Quantification of the impact of TOF and PSF on PET images using the noise-matching concept: clinical and phantom study

M Shekari, P Ghafarian, S Ahangari, MR Ay
Peer-reviewed Journal Publication
Nuclear Science and Techniques, 2017, Vol 28, pp 167

143.  Collimator-Detector Response Compensation in Molecular SPECT Reconstruction using STIR Framework?

Hojjat Mahani, Gholamreza Raisali, Alireza Kamali-Asl, Mohammad Reza Ay
Peer-reviewed Journal Publication
Iranian Journal of Nuclear Medicine and Molecular Imaging, 2017, Vol 25, pp 26-34

144.  Impact of Time-of-Flight and Point-Spread-Function for Respiratory Artifact Reduction in PET/CT Imaging: Focus on Standardized Uptake Value

Roya Sharifpour, Pardis Ghafarian, Mehrdad Bakhshayesh-Karam, Hamidreza Jamaati, Mohammad Reza Ay
Peer-reviewed Journal Publication
Tanaffos ,2017,Vol 16, pp 127

145.  Monte Carlo optimization of crystal configuration for pixelated molecular SPECT scanners

Hojjat Mahani, Gholamreza Raisali, Alireza Kamali-Asl, Mohammad Reza Ay
Peer-reviewed Journal Publication
Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, 2017, Vol 844, pp 1-6

146.  Single STE-MR Acquisition in MR-Based Attenuation Correction of Brain PET Imaging Employing a Fully Automated and Reproducible Level-Set Segmentation Approach

Anahita Fathi Kazerooni, Mohammad Reza Ay, Saman Arfaie, Parisa Khateri, Hamidreza Saligheh Rad
Peer-reviewed Journal Publication
Molecular Imaging & Biology, 2017, Vol 19, pp 143-152

147.  A hybrid tracking system for image-guided spine surgery using a tracked mobile C-arm: a phantom study

P. Ghobadi, A. Ahmadian, H. saberi, M.R. Ay, M. Addolghafar and K. Amini
Peer-reviewed Journal Publication
Turk J Elec Eng & Comp Sci, 2017, Vol. 25, pp 434-448.

148.  Development and Evaluation of Image Reconstruction Algorithms for a Novel Desktop SPECT System

Navid Zeraatkar, Arman Rahmim, Saeed Sarkar, Mohammad Reza Ay
Peer-reviewed Journal Publication
Asia Oceania Journal of Nuclear Medicine and Biology,2017, Vol 5,pp 120

149.  New approach for calibration of pixelated scintillation detectors of intraoperative gamma cameras

Afshin Akbarzadeh, Valiallah Saba, Mohammad Reza Ay
Peer-reviewed Journal Publication
Iranian Journal of Nuclear Medicine and Molecular Imaging, 2017, Vol. 25, No. 1, pp 34-42.

150.  MR-guided attenuation map for prostate PET-MRI: an intensity and morphologic-based segmentation approach for generating a five-class attenuation map in pelvic region

M. Shandiz, H. Saligeh Rad, P. Ghafarian, M. Bakhshaysh Karam and M.R. Ay
Peer-reviewed Journal Publication
Ann Nucl Med. 2017, Vol 31, pp 29-39

Abstract:

PURPOSE:

Prostate imaging is one of the major application of hybrid PET/MRI systems. Inaccurate attenuation maps (µ-maps) derived by direct segmentation (SEG) in which the cortical bone is ignored and the volume of the air in cavities is underestimated is the main challenge of commercial PET/MRI systems for the quantitative analysis of the pelvic region. The present study considered the cortical bone and air cavity along with soft tissue, fat, and background air in the µ-map of the pelvic region using a method based on SEG. The proposed method uses a dedicated imaging technique that increases the contrast between regions and a hybrid segmentation method to classify MR images based on intensity and morphologic characteristics of tissues, such as symmetry and similarity of bony structures.

PROCEDURES:

Ten healthy volunteers underwent MRI and ultra-low dose CT imaging. The dedicated MR imaging technique uses the short echo time (STE) based on the conventional sequencing implemented on a clinical 1.5T MRI scanner. The generation of a µ-map comprises the following steps: (1) bias field correction; (2) hybrid segmentation (HSEG), including segmenting images into clusters of cortical bone-air, soft tissue, and fat using spatial fuzzy c-means (SFCM), and separation of cortical bone and internal air cavities using morphologic characteristics; (3) the active contour approach for the separation of background air; and (4) the generation of a five-class μ-map for cortical bone, internal air cavity, soft tissue, fat tissue, and background air. Validation was done by comparison with segmented CT images.

RESULTS:

The Dice and sensitivity metrics of cortical bone structures and internal air cavities were 72 ± 11 and 66 ± 13 and 73 ± 10 and 68 ± 20 %, respectively. High correlation was observed between CT and HSEG-based µ-maps (R 2 > 0.99) and the corresponding sinograms (R 2 > 0.98).

CONCLUSIONS:

Currently, pelvis µ-maps provided by the current PET/MRI systems and the ultra-short echo time and atlas-based methods tend to be inaccurate. The proposed method acceptably generated a five-class μ-map using only one image.

KEYWORDS:

MRI-base attenuation correction; Morphologic characteristics-based segmentation; PET/MRI; Prostate imaging; STE pulse sequence

151.  Development and characterization of a compact hand-held gamma probe system, SURGEOGUIDE, based on NEMA NU3-2004 standards

S. Kaviani, N. Zeraatkar,S. Sajedi, N. Gorjizadeh, M.H. Farahani, P. Ghafarian,G. El Fakhri, H. Sabete and M.R. Ay
Peer-reviewed Journal Publication
Journal of Instrumentation, 2016, Vol 11

152.  Effect of TOF and PSF in detection of lymph node metastases in head and neck of PET/CT images

P Ghafarian, A Ketabi, A Doroudinia, M Bakhshayesh Karam, MR Ay
Proceeding and Conference Record
EUROPEAN JOURNAL OF NUCLEAR MEDICINE AND MOLECULAR IMAGING, 2016, Vol 43, pp s507

153.  Design and development of a dedicated portable gamma camera system for intra-operative imaging

S. Kaviani, N. Zeraatkar, S. Sajedi, A. Akbarzadeh, N. Gorjizadeh, M. H. Farahani, B. Teimourian, P. Ghafarian, H. Sabet and M.R. Ay
Peer-reviewed Journal Publication
Phys Med. 2016 Jul;32(7):889-97. doi: 10.1016/j.ejmp.2016.06.004. Epub 2016 Jun 23

Abstract

PURPOSE:

We developed a high performance portable gamma camera platform dedicated to identification of sentinel lymph nodes (SLNs) and radio-guided surgery for cancer patients. In this work, we present the performance characteristics of SURGEOSIGHT-I, the first version of this platform that can intra-operatively provide high-resolution images of the surveyed areas.

METHODS:

At the heart of this camera, there is a 43×43 array of pixelated sodium-activated cesium iodide (CsI(Na)) scintillation crystal with 1×1mm(2) pixel size and 5mm thickness coupled to a Hamamatsu H8500 flat-panel multi-anode (64 channels) photomultiplier tube. The probe is equipped with a hexagonal parallel-hole lead collimator with 1.2mm holes. The detector, collimator, and the associated front-end electronics are encapsulated in a common housing referred to as head.

RESULTS:

Our results show a count rate of ∼41kcps for 20% count loss. The extrinsic energy resolution was measured as 20.6% at 140keV. The spatial resolution and the sensitivity of the system on the collimator surface was measured as 2.2mm and 142cps/MBq, respectively. In addition, the integral and differential uniformity, after uniformity correction, in useful field-of-view (UFOV) were measured 4.5% and 4.6%, respectively.

CONCLUSIONS:

This system can be used for a number of clinical applications including SLN biopsy and radiopharmaceutical-guided surgery.

Keywords:

Sentinel lymph node (SLN), Lymphoscintigraphy, SURGEOSIGHT-I, Breast cancer, Intra-operative gamma camera

154.  Design, optimization and performance evaluation of BM-PET: A simulation study

Peyman Sheikhzadeh, Hamid Sabet, Hossein Ghadiri, Parham Geramifar, Pardis Ghafarian, Mohammad Reza Ay
Peer-reviewed Journal Publication
Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment

155.  Design and Assessment of a Novel SPECT System for Desktop Open-Gantry Imaging of Small Animals: a Monte Carlo Study

N. Zeraatkar, M. H. Farahani, S. Sarkar, A. Rahmim and M.R. Ay
Peer-reviewed Journal Publication
Med Phys. 2016 May;43(5):2581. doi: 10.1118/1.4947127

Abstract

PURPOSE:

Given increasing efforts in biomedical research utilizing molecular imaging methods, development of dedicated high-performance small-animal SPECT systems has been growing rapidly in the last decade. In the present work, we propose and assess an alternative concept for SPECT imaging enabling desktop open-gantry imaging of small animals.

METHODS:

The system, PERSPECT, consists of an imaging desk, with a set of tilted detector and pinhole collimator placed beneath it. The object to be imaged is simply placed on the desk. Monte Carlo (MC) and analytical simulations were utilized to accurately model and evaluate the proposed concept and design. Furthermore, a dedicated image reconstruction algorithm, finite-aperture-based circular projections (FABCP), was developed and validated for the system, enabling more accurate modeling of the system and higher quality reconstructed images. Image quality was quantified as a function of different tilt angles in the acquisition and number of iterations in the reconstruction algorithm. Furthermore, more complex phantoms including Derenzo, Defrise, and mouse whole body were simulated and studied.

RESULTS:

The sensitivity of the PERSPECT was 207 cps/MBq. It was quantitatively demonstrated that for a tilt angle of 30°, comparable image qualities were obtained in terms of normalized squared error, contrast, uniformity, noise, and spatial resolution measurements, the latter at ∼0.6 mm. Furthermore, quantitative analyses demonstrated that 3 iterations of FABCP image reconstruction (16 subsets/iteration) led to optimally reconstructed images.

CONCLUSIONS:

The PERSPECT, using a novel imaging protocol, can achieve comparable image quality performance in comparison with a conventional pinhole SPECT with the same configuration. The dedicated FABCP algorithm, which was developed for reconstruction of data from the PERSPECT system, can produce high quality images for small-animal imaging via accurate modeling of the system as incorporated in the forward- and back-projection steps. Meanwhile, the developed MC model and the analytical simulator of the system can be applied for further studies on development and evaluation of the system.

156.  Is Grid Therapy Useful for all Tumors and Every Grid Block Design?

S. Gholami, H. Nedaie, F. Longo, M. R. Ay, S. Wright and A. S. Meigooni
Peer-reviewed Journal Publication
J Appl Clin Med Phys. 2016 Mar 8;17(2):6015

Abstract

Grid therapy is a treatment technique that has been introduced for patients with advanced bulky tumors. The purpose of this study is to investigate the effect of the radiation sensitivity of the tumors and the design of the grid blocks on the clinical response of grid therapy. The Monte Carlo simulation technique is used to determine the dose distribution through a grid block that was used for a Varian 2100C linear accelerator. From the simulated dose profiles, the therapeutic ratio (TR) and the equivalent uniform dose (EUD) for different types of tumors with respect to their radiation sensitivities were calculated. These calculations were performed using the linear quadratic (LQ) and the Hug-Kellerer (H-K) models. The results of these calculations have been validated by comparison with the clinical responses of 232 patients from different publications, who were treated with grid therapy. These published results for different tumor types were used to examine the correlation between tumor radiosensitivity and the clinical response of grid therapy. Moreover, the influence of grid design on their clinical responses was investigated by using Monte Carlo simulations of grid blocks with different hole diameters and different center-to-center spacing. The results of the theoretical models and clinical data indicated higher clinical responses for the grid therapy on the patients with more radioresistant tumors. The differences between TR values for radioresistant cells and radiosensitive cells at 20 Gy and 10 Gy doses were up to 50% and 30%, respectively. Interestingly, the differences between the TR values with LQ model and H-K model were less than 4%. Moreover, the results from the Monte Carlo studies showed that grid blocks with a hole diameters of 1.0 cm and 1.25 cm may lead to about 19% higher TR relative to the grids with hole diameters smaller than 1.0 cm or larger than 1.25 cm (with 95% confidence interval). In sum-mary, the results of this study indicate that grid therapy is more effective for tumors with radioresistant characteristics than radiosensitive tumors.

157.  Reduction of Respiratory Induced Artefact in PET/CT Images using TOF Reconstruction

R. Sharif Pour, P. Ghafarian, A. Doroudinia, M. Bakhshayesh Karam and M. R. Ay
Published Abstract
ACNM 2016

Abstract

Objectives:

The aim of this study was to investigate the effect of time-of-flight (TOF) and point-spread function (PSF) for quantitative and qualitative PET/CT image analysis in relation to decrease respiratory artifact in diaphragmatic region.

Methods:

29 patients with uptake time 61±2 min and injection of 327.5 MBq (range 261–350 MBq) 18F-FDG were scanned with Discovery 690 GE PET/CT scanner, equipped with 64-slice CT. All of the lesions were in the diaphragmatic region including: the lung lower lobes, liver and stomach in patients with extended white band artefact. For quantitative measurement NEMA phantom were also utilized. The PET images were retrospectively reconstructed using HD (Fully 3D Iterative Reconstruction)+PSF and TOF+ PSF algorithm with various iterations, subsets and post smoothing filters. A semi-quantitative analysis was performed using SUVmax and SUVmean with 50% threshold. We also considered image quality using coefficient of variance (COV) in the liver in clinical study, the signal-to-noise ratio (SNR) and contrast to background measurements in each lesions. The PET/CT images reviewed by two expert physicians.

Results:

In the phantom study, SUVmean illustrated the more convenient value in related to SUVmax when TOF+PSF algorithm applied with increase of post filter from 4.4 mm to 6.4mm. In clinical study, the COV was decreased 7.4%±1.3% when TOF+PSF were compared with non-TOF image. The SUVmax trend to higher value with relative difference 11.3% (range: 0.5%–25.1%) when TOF and non-TOF images were evaluated. It was interesting that using appropriate TOF reconstruction parameter increased the SNR up 65.6% (Range: 7.0%–194.7%). The combination of TOF and PSF decreased the lesion size on PET images 33.0%, 25.7% and 24.5% in sagital, coronal and axial view respectively when compared with HD+PSF algorithm. According to balance among the SNR, contrast, noise and visual assessment, the optimal images were obtained with TOF+PSF with FWHM between 5.2 to 6.4 mm.

Conclusion:

A little overestimation in SUVmax versus to SUV mean 50% was observed, when PSF with combination of either VPHD or TOF was used. TOF with PSF improved white band artifact in diaphragmatic region remarkably, increased lesion delectability, and altered lesion size in PET images. It is noteworthy that the variation in SUV and lesion size is strongly dependent to the proximity of the lesions to the artefact region and it is highly recommended that to attain optimal image quality, combination of low iteration number and utilizing appropriate Gaussian filter is necessary because noise and false positive findings could be dominant with small-FWHM post filter.

158.  Hybrid Imaging, PET/CT, in HANDBOOK OF SMALL ANIMAL IMAGING, Preclinical Imaging, Therapy, and Applications

M.R. Ay and N. Ghazanfari
Book Chapter
George C. Kagadis et al. , Editors. 2016, Tylor & Francis Books, Inc.
Mohammad Reza Ay and Nafiseh Ghazanfari
Introduction to Combining MRI with PET

159.  Introducing the HeliGuide: Urea Breath Tests System for Detecting Helicobacter Pylori

Aram Radnia, MohammadHossein Farahani, C Hoorvash, MohammadReza Ay
Peer-reviewed Journal Publication
Frontiers in Biomedical Technologies,2015, Vol 2,pp 115-117

160.  How gamma camera’s head-tilts affect image quality of a nuclear scintigram?

Hojjat Mahani, Alireza Kamali-Asl, MohammadReza Ay
Peer-reviewed Journal Publication
Frontiers in Biomedical Technologies, 2015, Vol 1

161.  The influence of PET and CT misalignment due to respiratory motion on the cardiac PET/CT imaging: a simulation study

Pardis Ghafarian, MohammadReza Ay
Peer-reviewed Journal Publication
Frontiers in Biomedical Technologies,2015, Vol 1

162.  Acceptance Test of the first Hospital Cyclotron for Production of PET tracers in Iran

P. Ghafarian, S. M. Khamesi1, M. R. Golrokh Nodehi and M. R. Ay
Published Abstract
World Congress on Medical Physics & Biomedical Engineering, 7-12 June 2015, Toronto, Canada, p 518

163.  An alternate mathematical modeling of image formation, and framework for performance analysis of positioning algorithms in the scintillation camera

S. Hosseini, M. H. Farahani and M. R. Ay
Published Abstract
World Congress on Medical Physics & Biomedical Engineering, 7-12 June 2015, Toronto, Canada, p 103

164.  Can Pacemaker and ICD degrade CT-Based Attenuation Corrected cardiac SPECT images?

Z. Etemadi, A. Bitaran Rajabi, H. Malek, P. Ghafarian, N. Zeraatkar and M.R. Ay
Published Abstract
World Congress on Medical Physics & Biomedical Engineering, 7-12 June 2015, Toronto, Canada, p 132

165.  Correction of Metal Artefacts Induced from Pacemaker and ICD Leads in CT-Based Attenuation Correction of Cardiac SPECT data

M. R. Ay, Z. Etemadi, A. Bitarafan-Rajabi, H. Malek, N. Zeraatkar and P. Ghafarian
Published Abstract
World Congress on Medical Physics & Biomedical Engineering, 7-12 June 2015, Toronto, Canada, p 522

166.  Design, modeling and performance evaluation of a small animal Micro-CT scanner: A Monte Carlo study

S. Nezhaddehghani1, S. Sarkar, and M. R. Ay
Published Abstract
World Congress on Medical Physics & Biomedical Engineering, 7-12 June 2015, Toronto, Canada, p 97

167.  Generating a four-class attenuation map for MR-based attenuation correction of PET data in pelvis region using an automatic segmentation protocol

H. Saligheh Rad, M. Shirin Shandiz, P. Ghafarian, M. H. Arabi, M. Bakhshayeshkaram, N. Shafiei and M. R. Ay
Published Abstract
World Congress on Medical Physics & Biomedical Engineering, 7-12 June 2015, Toronto, Canada, p 201

168.  Generation of 4-Class Attenuation Map for MRI Based Attenuation Correction of PET Data in the Head Area Using a Novel Combination of STE/DIXON-MRI and FCM Clustering

P. Khateri, H. Saligheh Rad, A. Homayoun Jafari, A. Fathi, A. Akbarzadeh, M. Shojae Moghadam, A. Aryan, P. Ghafarian and M.R. Ay
Published Abstract
World Congress on Medical Physics & Biomedical Engineering, 7-12 June 2015, Toronto, Canada, p 371

169.  Impact of Point spread function modeling on tumor quantification in clinical PET/CT imaging

S. Ahangari1, P. Ghafarian, M. Bakhshayeshkaram and M. R. Ay
Published Abstract
World Congress on Medical Physics & Biomedical Engineering, 7-12 June 2015, Toronto, Canada, p 133

170.  Measurement of Photon and Neutron Dose Distribution in Cyclotron Bunker During F18 and N13 Production

P. Ghafarian, S. M. Khamesi, M. R. Golrokh Nodehi and M.R. Ay
Published Abstract
World Congress on Medical Physics & Biomedical Engineering, 7-12 June 2015, Toronto, Canada, p 606

171.  Monte Carlo Simulation of X-ray Spectra in Computed Tomography Scanner using GATE

M. R. Ay, S. Nezhaddehghani1, and S. Sarkar
Published Abstract
World Congress on Medical Physics & Biomedical Engineering, 7-12 June 2015, Toronto, Canada, p 331

172.  Optimal Pixelated Crystal for a Molecular SPECT Scanner: A GATE Monte Carlo Study

M. R. Ay, H. Mahani, G. Raisali, and A. Kamali-Asl
Published Abstract
World Congress on Medical Physics & Biomedical Engineering, 7-12 June 2015, Toronto, Canada, p 200

173.  Spinning Knife-Edge Slit-Hole: a Novel Collimation for High-Sensitivity Molecular SPECT

H. Mahani, G. Raisali, A. Kamali-Asl and M.R. Ay
Published Abstract
World Congress on Medical Physics & Biomedical Engineering, 7-12 June 2015, Toronto, Canada, p 200

174.  The Impact of time of flight algorithm and PSF modeling on standard uptake value in clinical PET/CT imaging

M. Shekari, P. Ghafarian, M. Bakhshayeshkaram and M. R. Ay
Published Abstract
World Congress on Medical Physics & Biomedical Engineering, 7-12 June 2015, Toronto, Canada, p 132