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Hegdé J, Tustison NJ, Parker WT, Branch F, Yanasak N, Stumpo LA. An Anatomical Template for the Normalization of Medical Images of Adult Human Hands. Diagnostics (Basel) 2023; 13:2010. [PMID: 37370905 DOI: 10.3390/diagnostics13122010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 06/01/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023] Open
Abstract
During medical image analysis, it is often useful to align (or 'normalize') a given image of a given body part to a representative standard (or 'template') of that body part. The impact that brain templates have had on the analysis of brain images highlights the importance of templates in general. However, templates for human hands do not exist. Image normalization is especially important for hand images because hands, by design, readily change shape during various tasks. Here we report the construction of an anatomical template for healthy adult human hands. To do this, we used 27 anatomically representative T1-weighted magnetic resonance (MR) images of either hand from 21 demographically representative healthy adult subjects (13 females and 8 males). We used the open-source, cross-platform ANTs (Advanced Normalization Tools) medical image analysis software framework, to preprocess the MR images. The template was constructed using the ANTs standard multivariate template construction workflow. The resulting template image preserved all the essential anatomical features of the hand, including all the individual bones, muscles, tendons, ligaments, as well as the main branches of the median nerve and radial, ulnar, and palmar metacarpal arteries. Furthermore, the image quality of the template was significantly higher than that of the underlying individual hand images as measured by two independent canonical metrics of image quality.
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Affiliation(s)
- Jay Hegdé
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Nicholas J Tustison
- Department of Radiology and Medical Imaging, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | - William T Parker
- Department of Radiology and Imaging, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Fallon Branch
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Nathan Yanasak
- Department of Radiology and Imaging, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Lorie A Stumpo
- Department of Radiology and Imaging, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
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Obuchowicz R, Oszust M, Piorkowski A. Interobserver variability in quality assessment of magnetic resonance images. BMC Med Imaging 2020; 20:109. [PMID: 32962651 PMCID: PMC7509933 DOI: 10.1186/s12880-020-00505-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 09/01/2020] [Indexed: 11/10/2022] Open
Abstract
Background The perceptual quality of magnetic resonance (MR) images influences diagnosis and may compromise the treatment. The purpose of this study was to evaluate how the image quality changes influence the interobserver variability of their assessment. Methods For the variability evaluation, a dataset containing distorted MRI images was prepared and then assessed by 31 experienced medical professionals (radiologists). Differences between observers were analyzed using the Fleiss’ kappa. However, since the kappa evaluates the agreement among radiologists taking into account aggregated decisions, a typically employed criterion of the image quality assessment (IQA) performance was used to provide a more thorough analysis. The IQA performance of radiologists was evaluated by comparing the Spearman correlation coefficients, ρ, between individual scores with the mean opinion scores (MOS) composed of the subjective opinions of the remaining professionals. Results The experiments show that there is a significant agreement among radiologists (κ=0.12; 95% confidence interval [CI]: 0.118, 0.121; P<0.001) on the quality of the assessed images. The resulted κ is strongly affected by the subjectivity of the assigned scores, separately presenting close scores. Therefore, the ρ was used to identify poor performance cases and to confirm the consistency of the majority of collected scores (ρmean = 0.5706). The results for interns (ρmean = 0.6868) supports the finding that the quality assessment of MR images can be successfully taught. Conclusions The agreement observed among radiologists from different imaging centers confirms the subjectivity of the perception of MR images. It was shown that the image content and severity of distortions affect the IQA. Furthermore, the study highlights the importance of the psychosomatic condition of the observers and their attitude.
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Affiliation(s)
- Rafal Obuchowicz
- Department of Diagnostic Imaging, Jagiellonian University Medical College, Kopernika Street 19, Cracow, 31-501, Poland
| | - Mariusz Oszust
- Department of Computer and Control Engineering, Rzeszow University of Technology, Wincentego Pola 2, Rzeszow, 35-959, Poland
| | - Adam Piorkowski
- Department of Biocybernetics and Biomedical Engineering, AGH University of Science and Technology, Mickiewicza 30, Cracow, 30-059, Poland.
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Bielecka M, Bielecki A, Obuchowicz R, Piórkowski A. Universal Measure for Medical Image Quality Evaluation Based on Gradient Approach. LECTURE NOTES IN COMPUTER SCIENCE 2020. [PMCID: PMC7303719 DOI: 10.1007/978-3-030-50423-6_30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In this paper, a new universal measure of medical images quality is proposed. The measure is based on the analysis of the image by using gradient methods. The number of isolated peaks in the examined image, as a function of the threshold value, is the basis of the assessment of the image quality. It turns out that for higher quality images the curvature of the graph of the said function has a higher value for lower threshold values. On the basis of the observed property, a new method of no-reference image quality assessment has been created. The experimental verification confirmed the method efficiency. The correlation between the arrangement depending on the image quality done by an expert and by using the proposed method is equal to 0.74. This means that the proposed method gives a correlation of higher than the best methods described in the literature. The proposed measure is useful to maximize the image quality while minimizing the time of medical examination.
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Obuchowicz R, Piórkowski A, Urbanik A, Strzelecki M. Influence of Acquisition Time on MR Image Quality Estimated with Nonparametric Measures Based on Texture Features. BIOMED RESEARCH INTERNATIONAL 2019; 2019:3706581. [PMID: 31828100 PMCID: PMC6886329 DOI: 10.1155/2019/3706581] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 08/06/2019] [Accepted: 09/01/2019] [Indexed: 12/21/2022]
Abstract
Correlation of parametrized image texture features (ITF) analyses conducted in different regions of interest (ROIs) overcomes limitations and reliably reflects image quality. The aim of this study is to propose a nonparametrical method and classify the quality of a magnetic resonance (MR) image that has undergone controlled degradation by using textural features in the image. Images of 41 patients, 17 women and 24 men, aged between 23 and 56 years were analyzed. T2-weighted sagittal sequences of the lumbar spine, cervical spine, and knee and T2-weighted coronal sequences of the shoulder and wrist were generated. The implementation of parallel imaging with the use of GRAPPA2, GRAPPA3, and GRAPPA4 led to a substantial reduction in the scanning time but also degraded image quality. The number of degraded image textural features was correlated with the scanning time. Longer scan times correlated with markedly higher ITF image persistence in comparison with images computed with reduced scan times. Higher ITF preservation was observed in images of bones in the spine and femur as compared to images of soft tissues, i.e., tendons and muscles. Finally, a nonparametrized image quality assessment based on an analysis of the ITF, computed for different tissues, correlating with the changes in acquisition time of the MR images, was successfully developed. The correlation between acquisition time and the number of reproducible features present in an MR image was found to yield the necessary assumptions to calculate the quality index.
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Affiliation(s)
- Rafał Obuchowicz
- Department of Diagnostic Imaging, Jagiellonian University Medical College, Kraków 31-501, Poland
| | - Adam Piórkowski
- Department of Biocybernetics and Biomedical Engineering, AGH University of Science and Technology, Kraków 30-059, Poland
| | - Andrzej Urbanik
- Department of Diagnostic Imaging, Jagiellonian University Medical College, Kraków 31-501, Poland
| | - Michał Strzelecki
- Institute of Electronics, Łódź University of Technology, Łódź 90-924, Poland
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Osadebey ME, Pedersen M, Arnold DL, Wendel-Mitoraj KE, Alzheimer's Disease Neuroimaging Initiative FT. Standardized quality metric system for structural brain magnetic resonance images in multi-center neuroimaging study. BMC Med Imaging 2018; 18:31. [PMID: 30223797 PMCID: PMC6142697 DOI: 10.1186/s12880-018-0266-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 07/31/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Multi-site neuroimaging offer several benefits and poses tough challenges in the drug development process. Although MRI protocol and clinical guidelines developed to address these challenges recommend the use of good quality images, reliable assessment of image quality is hampered by the several shortcomings of existing techniques. METHODS Given a test image two feature images are extracted. They are grayscale and contrast feature images. Four binary images are generated by setting four different global thresholds on the feature images. Image quality is predicted by measuring the structural similarity between appropriate pairs of binary images. The lower and upper limits of the quality index are 0 and 1. Quality prediction is based on four quality attributes; luminance contrast, texture, texture contrast and lightness. RESULTS Performance evaluation on test data from three multi-site clinical trials show good objective quality evaluation across MRI sequences, levels of distortion and quality attributes. Correlation with subjective evaluation by human observers is ≥ 0.6. CONCLUSION The results are promising for the evaluation of MRI protocols, specifically the standardization of quality index, designed to overcome the challenges encountered in multi-site clinical trials.
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Affiliation(s)
- Michael E Osadebey
- NeuroRx Research Inc, Montreal, 3575 Parc Avenue, Suite # 5322, Montreal, Quebec, H2X 3P9, Canada
| | - Marius Pedersen
- Department of Computer Science, Norwegian University of Science and Technology, Teknologivegen 22, Gjøvik, N-2815, Norway.
| | - Douglas L Arnold
- Montreal Neurological Institute and Hospital, McGill University, 3801 University St, Montreal, Quebec, H3A 2B4, Canada
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Osadebey M, Pedersen M, Arnold D, Wendel-Mitoraj K. Bayesian framework inspired no-reference region-of-interest quality measure for brain MRI images. J Med Imaging (Bellingham) 2017. [PMID: 28630885 DOI: 10.1117/1.jmi.4.2.025504] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We describe a postacquisition, attribute-based quality assessment method for brain magnetic resonance imaging (MRI) images. It is based on the application of Bayes theory to the relationship between entropy and image quality attributes. The entropy feature image of a slice is segmented into low- and high-entropy regions. For each entropy region, there are three separate observations of contrast, standard deviation, and sharpness quality attributes. A quality index for a quality attribute is the posterior probability of an entropy region given any corresponding region in a feature image where quality attribute is observed. Prior belief in each entropy region is determined from normalized total clique potential (TCP) energy of the slice. For TCP below the predefined threshold, the prior probability for a region is determined by deviation of its percentage composition in the slice from a standard normal distribution built from 250 MRI volume data provided by Alzheimer's Disease Neuroimaging Initiative. For TCP above the threshold, the prior is computed using a mathematical model that describes the TCP-noise level relationship in brain MRI images. Our proposed method assesses the image quality of each entropy region and the global image. Experimental results demonstrate good correlation with subjective opinions of radiologists for different types and levels of quality distortions.
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Affiliation(s)
- Michael Osadebey
- NeuroRx Research Inc., MRI Reader Group, Montreal, Québec, Canada
| | - Marius Pedersen
- Norwegian University of Science and Technology, Department of Computer Science, Gjøvik, Norway
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Gholipour A, Afacan O, Aganj I, Scherrer B, Prabhu SP, Sahin M, Warfield SK. Super-resolution reconstruction in frequency, image, and wavelet domains to reduce through-plane partial voluming in MRI. Med Phys 2016; 42:6919-32. [PMID: 26632048 DOI: 10.1118/1.4935149] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
PURPOSE To compare and evaluate the use of super-resolution reconstruction (SRR), in frequency, image, and wavelet domains, to reduce through-plane partial voluming effects in magnetic resonance imaging. METHODS The reconstruction of an isotropic high-resolution image from multiple thick-slice scans has been investigated through techniques in frequency, image, and wavelet domains. Experiments were carried out with thick-slice T2-weighted fast spin echo sequence on the Academic College of Radiology MRI phantom, where the reconstructed images were compared to a reference high-resolution scan using peak signal-to-noise ratio (PSNR), structural similarity image metric (SSIM), mutual information (MI), and the mean absolute error (MAE) of image intensity profiles. The application of super-resolution reconstruction was then examined in retrospective processing of clinical neuroimages of ten pediatric patients with tuberous sclerosis complex (TSC) to reduce through-plane partial voluming for improved 3D delineation and visualization of thin radial bands of white matter abnormalities. RESULTS Quantitative evaluation results show improvements in all evaluation metrics through super-resolution reconstruction in the frequency, image, and wavelet domains, with the highest values obtained from SRR in the image domain. The metric values for image-domain SRR versus the original axial, coronal, and sagittal images were PSNR = 32.26 vs 32.22, 32.16, 30.65; SSIM = 0.931 vs 0.922, 0.924, 0.918; MI = 0.871 vs 0.842, 0.844, 0.831; and MAE = 5.38 vs 7.34, 7.06, 6.19. All similarity metrics showed high correlations with expert ranking of image resolution with MI showing the highest correlation at 0.943. Qualitative assessment of the neuroimages of ten TSC patients through in-plane and out-of-plane visualization of structures showed the extent of partial voluming effect in a real clinical scenario and its reduction using SRR. Blinded expert evaluation of image resolution in resampled out-of-plane views consistently showed the superiority of SRR compared to original axial and coronal image acquisitions. CONCLUSIONS Thick-slice 2D T2-weighted MRI scans are part of many routine clinical protocols due to their high signal-to-noise ratio, but are often severely affected by through-plane partial voluming effects. This study shows that while radiologic assessment is performed in 2D on thick-slice scans, super-resolution MRI reconstruction techniques can be used to fuse those scans to generate a high-resolution image with reduced partial voluming for improved postacquisition processing. Qualitative and quantitative evaluation showed the efficacy of all SRR techniques with the best results obtained from SRR in the image domain. The limitations of SRR techniques are uncertainties in modeling the slice profile, density compensation, quantization in resampling, and uncompensated motion between scans.
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Affiliation(s)
- Ali Gholipour
- Department of Radiology, Boston Children's Hospital, Boston, Massachusetts 02115 and Harvard Medical School, Boston, Massachusetts 02115
| | - Onur Afacan
- Department of Radiology, Boston Children's Hospital, Boston, Massachusetts 02115 and Harvard Medical School, Boston, Massachusetts 02115
| | - Iman Aganj
- Radiology Department, Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, Massachusetts 02129 and Harvard Medical School, Boston, Massachusetts 02115
| | - Benoit Scherrer
- Department of Radiology, Boston Children's Hospital, Boston, Massachusetts 02115 and Harvard Medical School, Boston, Massachusetts 02115
| | - Sanjay P Prabhu
- Department of Radiology, Boston Children's Hospital, Boston, Massachusetts 02115 and Harvard Medical School, Boston, Massachusetts 02115
| | - Mustafa Sahin
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts 02115 and Harvard Medical School, Boston, Massachusetts 02115
| | - Simon K Warfield
- Department of Radiology, Boston Children's Hospital, Boston, Massachusetts 02115 and Harvard Medical School, Boston, Massachusetts 02115
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Jaspan ON, Fleysher R, Lipton ML. Compressed sensing MRI: a review of the clinical literature. Br J Radiol 2015; 88:20150487. [PMID: 26402216 DOI: 10.1259/bjr.20150487] [Citation(s) in RCA: 194] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
MRI is one of the most dynamic and safe imaging techniques available in the clinic today. However, MRI acquisitions tend to be slow, limiting patient throughput and limiting potential indications for use while driving up costs. Compressed sensing (CS) is a method for accelerating MRI acquisition by acquiring less data through undersampling of k-space. This has the potential to mitigate the time-intensiveness of MRI. The limited body of research evaluating the effects of CS on MR images has been mostly positive with regards to its potential as a clinical tool. Studies have successfully accelerated MRI with this technology, with varying degrees of success. However, more must be performed before its diagnostic efficacy and benefits are clear. Studies involving a greater number radiologists and images must be completed, rating CS based on its diagnostic efficacy. Also, standardized methods for determining optimal imaging parameters must be developed.
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Affiliation(s)
- Oren N Jaspan
- 1 Albert Einstein College of Medicine, The Bronx, NY, USA
| | - Roman Fleysher
- 2 The Gruss Magnetic Resonance Research Center, Department of Radiology, Albert Einstein College of Medicine, The Bronx, NY, USA
| | - Michael L Lipton
- 3 The Gruss Magnetic Resonance Research Center, Departments of Radiology, Psychiatry and Behavioral Sciences and The Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, The Bronx, NY, USA
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