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  1. Article: Protocol selection formalism for minimizing detectable differences in morphological radiomics features of lung lesions in repeated CT acquisitions.

    Zarei, Mojtaba / Abadi, Ehsan / Vancoillie, Liesbeth / Samei, Ehsan

    Journal of medical imaging (Bellingham, Wash.)

    2024  Volume 11, Issue 2, Page(s) 25501

    Abstract: Background: The accuracy of morphological radiomic features (MRFs) can be affected by various acquisition settings and imaging conditions. To ensure that clinically irrelevant changes do not reduce sensitivity to capture the radiomics changes between ... ...

    Abstract Background: The accuracy of morphological radiomic features (MRFs) can be affected by various acquisition settings and imaging conditions. To ensure that clinically irrelevant changes do not reduce sensitivity to capture the radiomics changes between successive acquisitions, it is essential to determine the optimal imaging systems and protocols to use.
    Purpose: The main goal of our study was to optimize CT protocols and minimize the minimum detectable difference (MDD) in successive acquisitions of MRFs.
    Method: MDDs were derived based on the previous research involving 15 realizations of nodule models at two different sizes. Our study involved simulations of two consecutive acquisitions using 297 different imaging conditions, representing variations in scanners' reconstruction kernels, dose levels, and slice thicknesses. Parametric polynomial models were developed to establish correlations between imaging system characteristics, lesion size, and MDDs. Additionally, polynomial models were used to model the correlation of the imaging system parameters. Optimization problems were formulated for each MRF to minimize the approximated function. Feature importance was determined for each MRF through permutation feature analysis. The proposed method was compared to the recommended guidelines by the quantitative imaging biomarkers alliance (QIBA).
    Results: The feature importance analysis showed that lesion size is the most influential parameter to estimate the MDDs in most of the MRFs. Our study revealed that thinner slices and higher doses had a measurable impact on reducing the MDDs. Higher spatial resolution and lower noise magnitude were identified as the most suitable or noninferior acquisition settings. Compared to QIBA, the proposed protocol selection guideline demonstrated a reduced coefficient of variation, with values decreasing from 1.49 to 1.11 for large lesions and from 1.68 to 1.12 for small lesions.
    Conclusion: The protocol optimization framework provides means to assess and optimize protocols to minimize the MDD to increase the sensitivity of the measurements in lung cancer screening.
    Language English
    Publishing date 2024-04-26
    Publishing country United States
    Document type Journal Article
    ISSN 2329-4302
    ISSN 2329-4302
    DOI 10.1117/1.JMI.11.2.025501
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Distinct atrophy of septal nuclei in Parkinson's disease.

    Kamalkhani, Niloufar / Zarei, Mojtaba

    Clinical parkinsonism & related disorders

    2022  Volume 7, Page(s) 100171

    Abstract: Objective: Parkinson's disease (PD) mainly affects basal ganglia including septal nuclei. Septal nuclei have extensive cholinergic connections with thalamus and brain stem nuclei. We hypothesized that the degeneration of septal nuclei has an impact on ... ...

    Abstract Objective: Parkinson's disease (PD) mainly affects basal ganglia including septal nuclei. Septal nuclei have extensive cholinergic connections with thalamus and brain stem nuclei. We hypothesized that the degeneration of septal nuclei has an impact on dopaminergic (motor) and non-dopaminergic (cognitive) symptoms in PD.
    Method: Clinical and MRI data of 80 patients with Parkinson's disease and 20 healthy controls (HC) with a structural magnetic resonance imaging (MRI) were selected from their first visit from PPMI database. Septal nuclei were manually segmented from T1W images according to previously established anatomical criteria. In addition, subcortical structures such as thalamus, amygdala, hippocampus, caudate, putamen, pallidum and accumbens were automatically segmented.
    Results: Volume of septal nuclei in the patients with PD was decreased in comparison with controls. These changes were independent of volume changes in other subcortical grey structure in PD. In addition, we found a correlation between motor components of unified Parkinson's disease rating scale (UPDRS) and volume of septal nuclei in PD. Other clinical measures such as olfactory test, upper extremity function (mobility) performance, total UPDRS, lower extremity function (mobility) performance, and cognitive function were significantly more in PD group than in control. No correction was found between cognitive function and volume of septal nuclei.
    Conclusion: We concluded that septal nuclei is distinctly affected in PD and is strongly associated with motor impairment. This may be a modulatory effect of cholinergic system on dopaminergic and glutamergic system. It is suggested that volume of septal nuclei may be a useful biomarker in PD diagnosis and monitoring.
    Language English
    Publishing date 2022-10-26
    Publishing country England
    Document type Journal Article
    ISSN 2590-1125
    ISSN (online) 2590-1125
    DOI 10.1016/j.prdoa.2022.100171
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  3. Article: Coronary stenosis quantification in cardiac computed tomography angiography: multi-factorial optimization of image quality and radiation dose.

    Zarei, Mojtaba / Abadi, Ehsan / Segars, William Paul / Samei, Ehsan

    Journal of medical imaging (Bellingham, Wash.)

    2023  Volume 10, Issue 6, Page(s) 63502

    Abstract: Background: The accuracy and variability of quantification in computed tomography angiography (CTA) are affected by the interplay of imaging parameters and patient attributes. The assessment of these combined effects has been an open engineering ... ...

    Abstract Background: The accuracy and variability of quantification in computed tomography angiography (CTA) are affected by the interplay of imaging parameters and patient attributes. The assessment of these combined effects has been an open engineering challenge.
    Purpose: In this study, we developed a framework that optimizes imaging parameters for accurate and consistent coronary stenosis quantification in cardiac CTA while accounting for patient-specific variables.
    Methods: The framework utilizes a task-specific image quality index, the estimability index (
    Results: The framework produced results consistent with imaging physics principles with approximated EPFs of 97% accuracy. The feature importance evaluation demonstrated a close match with earlier studies. The verification study found
    Conclusions: The protocol optimization framework provides means to assess and optimize CTA in terms of either image quality or radiation dose objectives with its results predicting prior clinical trial findings.
    Language English
    Publishing date 2023-12-27
    Publishing country United States
    Document type Journal Article
    ISSN 2329-4302
    ISSN 2329-4302
    DOI 10.1117/1.JMI.10.6.063502
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: A truth-based primal-dual learning approach to reconstruct CT images utilizing the virtual imaging trial platform.

    Zarei, Mojtaba / Sotoudeh-Paima, Saman / Abadi, Ehsan / Samei, Ehsan

    Proceedings of SPIE--the International Society for Optical Engineering

    2022  Volume 12031

    Abstract: Inherent to Computed tomography (CT) is image reconstruction, constructing 3D voxel values from noisy projection data. Modeling this inverse operation is not straightforward. Given the ill-posed nature of inverse problem in CT reconstruction, data-driven ...

    Abstract Inherent to Computed tomography (CT) is image reconstruction, constructing 3D voxel values from noisy projection data. Modeling this inverse operation is not straightforward. Given the ill-posed nature of inverse problem in CT reconstruction, data-driven methods need regularization to enhance the accuracy of the reconstructed images. Besides, generalization of the results hinges upon the availability of large training datasets with access to ground truth. This paper offers a new strategy to reconstruct CT images with the advantage of ground truth accessible through a virtual imaging trial (VIT) platform. A learned primal-dual deep neural network (LPD-DNN) employed the forward model and its adjoint as a surrogate of the imaging's geometry and physics. VIT offered simulated CT projections paired with ground truth labels from anthropomorphic human models without image noise and resolution degradation. The models included a library of anthropomorphic, computational patient models (XCAT). The DukeSim simulator was utilized to form realistic projection data emulating the impact of the physics and geometry of a commercial-equivalent CT scanner. The resultant noisy sinogram data associated with each slice was thus generated for training. Corresponding linear attenuation coefficients of phantoms' materials at the effective energy of the x-ray spectrum were used as the ground truth labels. The LPD-DNN was deployed to learn the complex operators and hyper-parameters in the proximal primal-dual optimization. The obtained validation results showed a 12% normalized root mean square error with respect to the ground truth labels, a peak signal-to-noise ratio of 32 dB, a signal-to-noise ratio of 1.5, and a structural similarity index of 96%. These results were highly favorable compared to standard filtered-back projection reconstruction (65%, 17 dB, 1.0, 26%).
    Language English
    Publishing date 2022-04-04
    Publishing country United States
    Document type Journal Article
    ISSN 0277-786X
    ISSN 0277-786X
    DOI 10.1117/12.2613168
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Cognitive theories of autism based on the interactions between brain functional networks.

    Alamdari, Sarah Barzegari / Sadeghi Damavandi, Masoumeh / Zarei, Mojtaba / Khosrowabadi, Reza

    Frontiers in human neuroscience

    2022  Volume 16, Page(s) 828985

    Abstract: Cognitive functions are directly related to interactions between the brain's functional networks. This functional organization changes in the autism spectrum disorder (ASD). However, the heterogeneous nature of autism brings inconsistency in the findings, ...

    Abstract Cognitive functions are directly related to interactions between the brain's functional networks. This functional organization changes in the autism spectrum disorder (ASD). However, the heterogeneous nature of autism brings inconsistency in the findings, and specific pattern of changes based on the cognitive theories of ASD still requires to be well-understood. In this study, we hypothesized that the theory of mind (ToM), and the weak central coherence theory must follow an alteration pattern in the network level of functional interactions. The main aim is to understand this pattern by evaluating interactions between all the brain functional networks. Moreover, the association between the significantly altered interactions and cognitive dysfunctions in autism is also investigated. We used resting-state fMRI data of 106 subjects (5-14 years, 46 ASD: five female, 60 HC: 18 female) to define the brain functional networks. Functional networks were calculated by applying four parcellation masks and their interactions were estimated using Pearson's correlation between pairs of them. Subsequently, for each mask, a graph was formed based on the connectome of interactions. Then, the local and global parameters of the graph were calculated. Finally, statistical analysis was performed using a two-sample
    Language English
    Publishing date 2022-10-06
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2425477-0
    ISSN 1662-5161
    ISSN 1662-5161
    DOI 10.3389/fnhum.2022.828985
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  6. Article ; Online: Stroke Associated with COVID-19 Vaccines.

    Kakovan, Maryam / Ghorbani Shirkouhi, Samaneh / Zarei, Mojtaba / Andalib, Sasan

    Journal of stroke and cerebrovascular diseases : the official journal of National Stroke Association

    2022  Volume 31, Issue 6, Page(s) 106440

    Abstract: Objectives: Development of safe and effective vaccines against coronavirus disease 2019 (COVID-19) remains the cornerstone of controlling this pandemic. However, there are increasing reports of various types of stroke including ischemic stroke, and ... ...

    Abstract Objectives: Development of safe and effective vaccines against coronavirus disease 2019 (COVID-19) remains the cornerstone of controlling this pandemic. However, there are increasing reports of various types of stroke including ischemic stroke, and hemorrhagic stroke, as well as cerebral venous sinus thrombosis (CVST) after COVID-19 vaccination. This paper aims to review reports of stroke associated with COVID-19 vaccines and provide a coherent clinical picture of this condition.
    Materials and methods: A literature review was performed with a focus on data from recent studies.
    Results: Most of such patients are women under 60 years of age and who had received ChAdOx1 nCoV-19 vaccine. Most studies reported CVST with or without secondary ischemic or hemorrhagic stroke, and some with Vaccine-induced Thrombotic Thrombocytopenia (VITT). The most common clinical symptom of CVST seen after COVID-19 vaccination was headache. The clinical course of CVST after COVID-19 vaccination may be more severe than CVST not associated with COVID vaccination. Management of CVST following COVID-19 vaccination is challenging and may differ from the standard treatment of CVST. Low molecular weight heparin is commonly used in the treatment of CVST; however, it may worsen outcomes in CVST associated with VITT. Furthermore, administration of intravenous immunoglobulin and high-dose glucocorticoids have been recommended with various success rates.
    Conclusion: These contradictory observations are a source of confusion in clinical decision-making and warrant further study and development of clinical guidelines. Clinicians should be aware of clinical presentation, diagnosis, and management of stroke associated with COVID-19 vaccination.
    MeSH term(s) COVID-19/prevention & control ; COVID-19 Vaccines/adverse effects ; ChAdOx1 nCoV-19 ; Female ; Hemorrhagic Stroke/chemically induced ; Hemorrhagic Stroke/epidemiology ; Humans ; Ischemic Stroke/chemically induced ; Ischemic Stroke/epidemiology ; Male ; SARS-CoV-2 ; Thrombocytopenia
    Chemical Substances COVID-19 Vaccines ; ChAdOx1 nCoV-19 (B5S3K2V0G8)
    Language English
    Publishing date 2022-03-04
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 1131675-5
    ISSN 1532-8511 ; 1052-3057
    ISSN (online) 1532-8511
    ISSN 1052-3057
    DOI 10.1016/j.jstrokecerebrovasdis.2022.106440
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Harmonizing CT Images via Physics-based Deep Neural Networks.

    Zarei, Mojtaba / Sotoudeh-Paima, Saman / McCabe, Cindy / Abadi, Ehsan / Samei, Ehsan

    Proceedings of SPIE--the International Society for Optical Engineering

    2023  Volume 12463

    Abstract: The rendition of medical images influences the accuracy and precision of quantifications. Image variations or biases make measuring imaging biomarkers challenging. The objective of this paper is to reduce the variability of computed tomography (CT) ... ...

    Abstract The rendition of medical images influences the accuracy and precision of quantifications. Image variations or biases make measuring imaging biomarkers challenging. The objective of this paper is to reduce the variability of computed tomography (CT) quantifications for radiomics and biomarkers using physics-based deep neural networks (DNNs). With the proposed framework, it is possible to harmonize the different renditions of a single CT scan (with variations in reconstruction kernel and dose) into an image that is in close agreement with the ground truth. To this end, a generative adversarial network (GAN) model was developed where the generator is informed by the scanner's modulation transfer function (MTF). To train the network, a virtual imaging trial (VIT) platform was used to acquire CT images, from a set of forty computational models (XCAT) serving as the patient model. Phantoms with varying levels of pulmonary disease, such as lung nodules and emphysema, were used. We scanned the patient models with a validated CT simulator (DukeSim) modeling a commercial CT scanner at 20 and 100 mAs dose levels and then reconstructed the images by twelve kernels representing smooth to sharp kernels. An evaluation of the harmonized virtual images was conducted in four different ways: 1) visual quality of the images, 2) bias and variation in density-based biomarkers, 3) bias and variation in morphological-based biomarkers, and 4) Noise Power Spectrum (NPS) and lung histogram. The trained model harmonized the test set images with a structural similarity index of 0.95±0.1, a normalized mean squared error of 10.2±1.5%, and a peak signal-to-noise ratio of 31.8±1.5 dB. Moreover, emphysema-based imaging biomarkers of LAA-950 (-1.5±1.8), Perc15 (13.65±9.3), and Lung mass (0.1±0.3) had more precise quantifications.
    Language English
    Publishing date 2023-04-07
    Publishing country United States
    Document type Journal Article
    ISSN 0277-786X
    ISSN 0277-786X
    DOI 10.1117/12.2654215
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  8. Article: A systematic assessment of photon-counting CT for bone mineral density and microarchitecture quantifications.

    McCabe, Cindy / Sauer, Thomas J / Zarei, Mojtaba / Segars, W Paul / Samei, Ehsan / Abadi, Ehsan

    Proceedings of SPIE--the International Society for Optical Engineering

    2023  Volume 12463

    Abstract: Photon-counting CT (PCCT) is an emerging imaging technology with potential improvements in quantification and rendition of micro-structures due to its smaller detector sizes. The aim of this study was to assess the performance of a new PCCT scanner ( ... ...

    Abstract Photon-counting CT (PCCT) is an emerging imaging technology with potential improvements in quantification and rendition of micro-structures due to its smaller detector sizes. The aim of this study was to assess the performance of a new PCCT scanner (NAEOTOM Alpha, Siemens) in quantifying clinically relevant bone imaging biomarkers for characterization of common bone diseases. We evaluated the ability of PCCT in quantifying microarchitecture in bones compared to conventional energy-integrating CT. The quantifications were done through virtual imaging trials, using a 50 percentile BMI male virtual patient, with a detailed model of trabecular bone with varied bone densities in the lumbar spine. The virtual patient was imaged using a validated CT simulator (DukeSim) at CTDI
    Language English
    Publishing date 2023-04-07
    Publishing country United States
    Document type Journal Article
    ISSN 0277-786X
    ISSN 0277-786X
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  9. Article ; Online: White matter abnormalities in paediatric obsessive-compulsive disorder: a systematic review of diffusion tensor imaging studies.

    Haghshomar, Maryam / Mirghaderi, Seyed Peyman / Shobeiri, Parnian / James, Anthony / Zarei, Mojtaba

    Brain imaging and behavior

    2023  Volume 17, Issue 3, Page(s) 343–366

    Abstract: Microstructural alterations in white matter are evident in obsessive-compulsive disorder (OCD) both in adult and paediatric populations. Paediatric patients go through the process of maturation and thus may undergo different pathophysiology than adult ... ...

    Abstract Microstructural alterations in white matter are evident in obsessive-compulsive disorder (OCD) both in adult and paediatric populations. Paediatric patients go through the process of maturation and thus may undergo different pathophysiology than adult OCD. Findings from studies in paediatric obsessive-compulsive disorder have been inconsistent, possibly due to their small sample size or heterogeneous populations. The aim of this review is to provide a comprehensive overview of white matter structures in paediatric obsessive-compulsive disorder and their correlation with clinical features. Based on PRISMA guidelines, we performed a systematic search on diffusion tensor imaging studies that reported fractional anisotropy, mean diffusivity, radial diffusivity, or axial diffusivity alterations between paediatric patients with obsessive-compulsive disorder and healthy controls using voxel-based analysis, or tract-based spatial statistics. We identified fifteen relevant studies. Most studies reported changes predominantly in the corpus callosum, cingulum, arcuate fasciculus, uncinate fasciculus, inferior longitudinal fasciculus, superior longitudinal fasciculus, inferior fronto-occipital fasciculus, corticospinal tract, forceps minor and major, and the cerebellum in paediatric obsessive-compulsive disorder. These alterations included increased and decreased fractional anisotropy and radial diffusivity, and increased mean and axial diffusivity in different white matter tracts. These changes were associated with obsessive-compulsive disorder symptoms. Moreover, specific genetic polymorphisms were linked with cerebellar white matter changes in paediatric obsessive-compulsive disorder. White matter changes are widespread in paediatric OCD patients. These changes are often associated with symptoms however there are controversies in the direction of changes in some tracts.
    MeSH term(s) Adult ; Humans ; Child ; Diffusion Tensor Imaging/methods ; White Matter/diagnostic imaging ; Magnetic Resonance Imaging ; Diffusion Magnetic Resonance Imaging ; Obsessive-Compulsive Disorder/diagnostic imaging ; Anisotropy ; Brain/diagnostic imaging
    Language English
    Publishing date 2023-03-20
    Publishing country United States
    Document type Systematic Review ; Journal Article ; Review
    ZDB-ID 2377165-3
    ISSN 1931-7565 ; 1931-7557
    ISSN (online) 1931-7565
    ISSN 1931-7557
    DOI 10.1007/s11682-023-00761-x
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  10. Article ; Online: Study of structural network connectivity using DTI tractography in insomnia disorder.

    Rostampour, Masoumeh / Gharaylou, Zeinab / Rostampour, Ali / Shahbodaghy, Fatemeh / Zarei, Mojtaba / Fadaei, Reza / Khazaie, Habibolah

    Psychiatry research. Neuroimaging

    2023  Volume 336, Page(s) 111730

    Abstract: Most of tractography studies on insomnia disorder (ID) have reported decreased structural connectivity between cortical and subcortical structures. Tractography based on standard diffusion tensor imaging (DTI) can generate high number of false-positive ... ...

    Abstract Most of tractography studies on insomnia disorder (ID) have reported decreased structural connectivity between cortical and subcortical structures. Tractography based on standard diffusion tensor imaging (DTI) can generate high number of false-positive streamlines connections between gray matter regions. In the present study, we employed the convex optimization modeling for microstructure informed tractography-2 (COMMIT2) to improve the accuracy of the reconstructed whole-brain connectome and filter implausible brain connections in 28 patients with ID and compared with 27 healthy controls. Then, we used NBS-predict (a prediction-based extension to the network-based statistic method) in the COMMIT2-weighted connectome. Our results revealed decreased structural connectivity between subregions of the left somatomotor, ventral attention, frontoparietal, dorsal attention and default mode networks in the insomnia group. Moreover, there is a negative correlation between sleep efficiency and structural connectivity within the left frontoparietal, visual, default mode network, limbic, dorsal attention, right dorsal attention as well as right default mode networks. By comparing with standard connectivity analysis, we showed that by removing of false-positive streamlines connections after COMMIT2 filtering, abnormal structural connectivity was reduced in patients with ID compared to controls. Our results demonstrate the importance of improving the accuracy of tractography for understanding structural connectivity networks in ID.
    MeSH term(s) Humans ; Diffusion Tensor Imaging/methods ; Sleep Initiation and Maintenance Disorders/diagnostic imaging ; Brain ; Gray Matter ; Connectome/methods
    Language English
    Publishing date 2023-10-19
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 445361-x
    ISSN 1872-7506 ; 1872-7123 ; 0925-4927 ; 0165-1781
    ISSN (online) 1872-7506 ; 1872-7123
    ISSN 0925-4927 ; 0165-1781
    DOI 10.1016/j.pscychresns.2023.111730
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