Convolutional Neural Networks and Geometric Moments to Identify the Bilateral Symmetric Midplane in Facial Skeletons from CT Scans
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Data Processing
2.2. CNN Architecture and Implementation Details
2.2.1. CNN Framework for Biomedical Image Segmentation
2.2.2. CNN Framework for Rotation Invariant
2.3. Model Performance Evaluation and Statistical Analysis
2.4. 3D Geometric Moments
3. Results and Discussion
3.1. Skull Segmentation
3.2. Transverse and Coronal Angles
3.3. Geometric Moments Image Center
3.4. Deformed Skull Test
- the small database size, which is already reported in [27];
- to the best of our knowledge, there are no deformed CT database available which restricts the possibility to train the system with deformed images;
- during the ground truth segmentation process and voxelization, a few regions of interest (ROIs) may have not been incorporated in the 3D model. The first may be caused by the manual selection of the ROI, performed by an expert, which leads to the CNN generating the defects. Secondly, a quantity of information from the skull voxel may be lost due to the smoothing of the edges and noise residuals removal performed in the segmentation process;
- regarding the center of the 3D images, as reported by [8], when the image suffers from a lack of symmetry, non-uniform brightness, deformation, interference, or incompleteness, the calculation of the image center using geometric moments becomes complex and finds some restrictions as this technique is a quantitative measure of an image’s function or structure.
4. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
AD | average difference |
CNN | convolutional neural network |
CT | computerized tomography |
DSC | dice similarity coefficient |
FN | false negative |
FP | false positive |
GB | gigabyte |
GPUs | graphics processing units |
HD | hausdorff distance |
ICP | iterative closest point |
IQI | image quality index |
LMSE | laplacian mean square error |
MD | maximum difference |
MRI | magnetic resonance imaging |
MSE | mean-square error |
MSP | midsagittal plane |
NAE | normalized absolute error |
NK | normalized cross-correlation |
NPV | negative predictive value |
PCA | principal component analysis |
PPV | positive predictive value |
ROIs | regions of interest |
SC | structural content |
SD | standard deviation |
SSIM | structural similarity index |
STL | standard tessellation language |
SVD | symmetric volume difference |
TP | true positive |
References
- Damstra, J.; Fourie, Z.; De Wit, M.; Ren, Y. A three-dimensional comparison of a morphometric and conventional cephalometric midsagittal planes for craniofacial asymmetry. Clin. Oral Investig. 2011, 16, 285–294. [Google Scholar] [CrossRef] [Green Version]
- Kim, T.-Y.; Baik, J.-S.; Park, J.-Y.; Chae, H.-S.; Huh, K.-H.; Choi, S.-C. Determination of midsagittal plane for evaluation of facial asymmetry using three-dimensional computed tomography. Imaging Sci. Dent. 2011, 41, 79–84. [Google Scholar] [CrossRef] [Green Version]
- Willing, R.; Roumeliotis, G.; Jenkyn, T.; Yazdani, A. Development and evaluation of a semi-automatic technique for determining the bilateral symmetry plane of the facial skeleton. Med. Eng. Phys. 2013, 35, 1843–1849. [Google Scholar] [CrossRef]
- Roumeliotis, G.; Willing, R.; Neuert, M.; Ahluwali, R.; Jenkyn, T.; Yazdani, A. Application of a novel semi-automatic technique for determining the bilateral symmetry plane of the facial skeleton of normal adult males. J. Craniofacial Surg. 2015, 26, 1997–2001. [Google Scholar] [CrossRef]
- Di Angelo, L.; Stefano, P.D.; Governi, L.; Marzola, A.; Volpe, Y. A robust and automatic method for the best symmetry plane detection of craniofacial skeletons. Symmetry 2019, 11, 245. [Google Scholar] [CrossRef]
- Di Angelo, L.; Di Stefano, P. A computational method for bilateral symmetry recognition in asymmetrically scanned human faces. Comput. Aided Des. Appl. 2014, 11, 275–283. [Google Scholar] [CrossRef]
- Noori, S.M.R.; Farnia, P.; Bayat, M.; Bahrami, N.; Shakourirad, A.; Ahmadian, A. Automatic detection of symmetry plane for computer-aided surgical simulation in craniomaxillofacial surgery. Phys. Eng. Sci. Med. 2020, 43, 1087–1099. [Google Scholar] [CrossRef]
- Dalvit Carvalho da Silva, R.; Jenkyn, T.R.; Carranza, V.A. Application of a novel automatic method for determining the bilateral symmetry midline of the facial skeleton based on invariant moments. Symmetry 2020, 12, 1448. [Google Scholar] [CrossRef]
- Chilamkurthy, S.; Ghosh, R.; Tanamala, S.; Biviji, M.; Campeau, N.G.; Venugopal, V.K.; Mahajan, V.; Rao, P.; Warier, P. Deep learning algorithms for detection of critical findings in head CT scans: A retrospective study. Lancet 2018, 392, 2388–2396. [Google Scholar] [CrossRef]
- Patil, S.; Ravi, B. Voxel-based representation, display and thickness analysis of intricate shapes. In Proceedings of the Ninth International Conference on Computer Aided Design and Computer Graphics (CAD-CG’05), Hong Kong, China, 7–10 December 2005; p. 6. [Google Scholar] [CrossRef]
- Ronneberger, O.; Fischer, P.; Brox, T. U-Net: Convolutional networks for biomedical image segmentation. arXiv 2015, arXiv:1505.04597. [Google Scholar]
- Kim, T.; Lee, K.; Ham, S.; Park, B.; Lee, S.; Hong, D.; Kim, G.B.; Kyung, Y.S.; Kim, C.-S.; Kim, N. Active learning for accuracy enhancement of semantic segmentation with CNN-corrected label curations: Evaluation on kidney segmentation in abdominal CT. Sci. Rep. 2020, 10, 1–7. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Aldoj, N.; Biavati, F.; Michallek, F.; Stober, S.; Dewey, M. Automatic prostate and prostate zones segmentation of magnetic resonance images using DenseNet-like U-net. Sci. Rep. 2020, 10, 1–17. [Google Scholar] [CrossRef]
- Dong, H.; Yang, G.; Liu, F.; Mo, Y.; Guo, Y. Automatic brain tumor detection and segmentation using U-Net based fully convolutional networks. In Medical Image Understanding and Analysis; Valdés Hernández, M., González-Castro, V., Eds.; Communications in Computer and Information Science; Springer: Cham, Switzerland, 2017; Volume 723. [Google Scholar] [CrossRef] [Green Version]
- Lee, B.; Yamanakkanavar, N.; Choi, J.Y. Automatic segmentation of brain MRI using a novel patch-wise U-net deep architecture. PLoS ONE 2020, 15, e0236493. [Google Scholar] [CrossRef]
- Çiçek, Ö.; Abdulkadir, A.; Lienkamp, S.S.; Brox, T.; Ronneberger, O. 3D U-Net: Learning dense volumetric segmentation from sparse annotation. arXiv 2016, arXiv:1606.06650. [Google Scholar]
- Chen, Y.; Lyu, Z.X.; Kang, X.; Wang, Z.J. A rotation-invariant convolutional neural network for image enhancement forensics. In Proceedings of the 2018 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), Calgary, AB, Canada, 15–20 April 2018; pp. 2111–2115. [Google Scholar]
- Chidester, B.; Zhou, T.; Do, M.N.; Ma, J. Rotation equivariant and invariant neural networks for microscopy image analysis. Bioinformatics 2019, 35, i530–i537. [Google Scholar] [CrossRef] [PubMed]
- Kim, J.; Jung, W.; Kim, H.; Lee, J. CyCNN: A rotation invariant CNN using polar mapping and cylindrical convolutional layers. arXiv 2020, arXiv:2007.10588. [Google Scholar]
- Dice, L.R. Measures of the amount of ecologic association between species. Ecology 1945, 26, 297–302. [Google Scholar] [CrossRef]
- Schenk, A.; Prause, G.; Peitgen, H.-O. Efficient semiautomatic segmentation of 3D objects in medical images. In Medical Image Computing and Computer-Assisted Intervention—MICCAI 2000; Delp, S.L., DiGoia, A.M., Jaramaz, B., Eds.; Lecture Notes in Computer Science; Springer: Berlin/Heidelberg, Germany, 2000; Volume 1935, pp. 186–195. [Google Scholar]
- Yeghiazaryan, V.; Voiculescu, I. Family of boundary overlap metrics for the evaluation of medical image segmentation. J. Med. Imaging 2018, 5, 1. [Google Scholar] [CrossRef]
- Vania, M.; Mureja, D.; Lee, D. Automatic spine segmentation from CT images using Convolutional Neural Network via redundant generation of class labels. J. Comput. Des. Eng. 2019, 6, 224–232. [Google Scholar] [CrossRef]
- Mercimek, M.; Gulez, K.; Mumcu, T.V. Real object recognition using moment invariants. Sadhana 2005, 30, 765–775. [Google Scholar] [CrossRef] [Green Version]
- Xu, D.; Li, H. Geometric moment invariants. Pattern Recognit. 2008, 41, 240–249. [Google Scholar] [CrossRef]
- Minnema, J.; Van Eijnatten, M.; Kouw, W.M.; Diblen, F.; Mendrik, A.; Wolff, J. CT image segmentation of bone for medical additive manufacturing using a convolutional neural network. Comput. Biol. Med. 2018, 103, 130–139. [Google Scholar] [CrossRef] [Green Version]
- Kodym, O.; Španěl, M.; Herout, A. Segmentation of defective skulls from CT data for tissue modelling. arXiv 2019, arXiv:1911.08805. [Google Scholar]
- Adam, A. Converting a 3D logical array into an STL surface mesh. Available online: https://www.mathworks.com/matlabcentral/fileexchange/27733-converting-a-3d-logical-array-into-an-stl-surface-mesh (accessed on 1 November 2020).
- Kinahan, P.; Muzi, M.; Bialecki, B.; Coombs, L. Data from ACRIN-FMISO brain. Cancer Imaging Arch. 2018. [Google Scholar] [CrossRef]
- Gerstner, E.R.; Zhang, Z.; Fink, J.R.; Muzi, M.; Hanna, L.; Greco, E.; Prah, M.; Schmainda, K.M.; Mintz, A.; Kostakoglu, L.; et al. ACRIN 6684: Assessment of tumor hypoxia in newly diagnosed glioblastoma using 18F-FMISO PET and MRI. Clin. Cancer Res. 2016, 22, 5079–5086. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Ratai, E.-M.; Zhang, Z.; Fink, J.; Muzi, M.; Hanna, L.; Greco, E.; Richards, T.; Kim, D.; Andronesi, O.C.; Mintz, A.; et al. ACRIN 6684: Multicenter, phase II assessment of tumor hypoxia in newly diagnosed glioblastoma using magnetic resonance spectroscopy. PLoS ONE 2018, 13, e0198548. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Zuley, M.L.; Jarosz, R.; Kirk, S.; Lee, Y.; Colen, R.; Garcia, K.; Aredes, N.D. Radiology data from the cancer genome atlas head-neck squamous cell carcinoma [tcga-hnsc] collection. Cancer Imaging Arch. 2016. [Google Scholar] [CrossRef]
- Clark, K.; Vendt, B.; Smith, K.; Freymann, J.; Kirby, J.; Koppel, P.; Moore, S.; Phillips, S.; Maffitt, D.; Pringle, M.; et al. The Cancer Imaging Archive (TCIA): Maintaining and operating a public information repository. J. Digit. Imaging 2013, 26, 1045–1057. [Google Scholar] [CrossRef] [Green Version]
Parameter | Value |
---|---|
Optimizer | Adam |
Encoder Depth | 4 |
Filter Size | 5 |
Number of First Encoder Filter | 6 |
Patch Per Image | 4 |
Min Batch Size | 128 |
Initial Learning Rate | 10−2 |
Layers | Size | Number Filter | Stride | |
---|---|---|---|---|
3D Conv | 1 × 1 | 3 | 1 | |
1 | BN + Relu | - | - | - |
3D Max pooling | 5 × 5 | - | 2 | |
3D Conv | 5 × 5 | 8 | 1 | |
2 | BN + Relu | - | - | - |
3D Max pooling | 5 × 5 | - | 2 | |
3D Conv | 7 × 7 | 16 | 1 | |
3 | BN + Relu | - | - | - |
3D Max pooling | 3 × 3 | - | 2 | |
3D Conv | 5 × 5 | 32 | 1 | |
4 | BN + Relu | - | - | - |
3D Max pooling | 2 × 2 | - | 2 | |
3D Conv | 5 × 5 | 64 | 1 | |
5 | BN + Relu | - | - | - |
3D Average pooling | 2 × 2 | - | 2 | |
6 | 3D Conv | 1 × 1 | 128 | 1 |
BN + Relu | - | - | - | |
7 | FC (25 neurons) | - | - | - |
Relu | - | - | - | |
8 | FC (50 neurons) | - | - | - |
Relu | - | - | - | |
9 | FC (labels neurons) | - | - | - |
Softmax | - | - | - |
DSC-Skull | DSC-Background | SVD-Skull | HD-Skull |
---|---|---|---|
0.8993 ± 0.004 | 0.9927 ± 0.0003 | 0.1007 ± 0.004 | 67.7 ± 09.20 |
0.9093 ± 0.008 | 0.9948 ± 0.0005 | 0.0907 ± 0.008 | 27.81 ± 31.19 |
0.9150 ± 0.008 | 0.9941 ± 0.0006 | 0.0850 ± 0.008 | 38.78 ± 20.26 |
0.9349 ± 0.008 | 0.9958 ± 0.0005 | 0.0651 ± 0.008 | 49.92 ± 37.69 |
0.9362 ± 0.006 | 0.9953 ± 0.0004 | 0.8844 ± 0.006 | 39.99 ± 44.40 |
0.9189 ± 0.016 | 0.9945 ± 0.0012 | 0.0811 ± 0.016 | 44.73 ± 14.79 |
Index | Ideal Value | Coronal CNN Value | Transverse CNN Value |
---|---|---|---|
Accuracy | 1 | 0.9909 ± 0.0038 | 0.9947 ± 0.0034 |
Sensitivity | 1 | 0.9811 ± 0.0170 | 0.9969 ± 0.0054 |
Specificity | 1 | 0.9982 ± 0.0012 | 0.9994 ± 0.0005 |
PPV | 1 | 0.9646 ± 0.0236 | 0.9892 ± 0.0106 |
NPV | 1 | 0.991 ± 0.0009 | 0.9998 ± 0.0003 |
AD | 0 | 0.0124 ± 0.0085 | 0.0004 ± 0.0095 |
IQI | 1 | 0.9979 ± 0.0014 | 0.9994 ± 0.0004 |
LMSE | 0 | 0.9926 ± 0.6717 | 0.9571 ± 0.0814 |
MD | 0 | 11.667 ± 1.1547 | 9.3333 ± 5.6862 |
MSE | 0 | 0.2710 ± 0.1883 | 0.0723 ± 0.0561 |
NAE | 0 | 0.0030 ± 0.0018 | 0.0012 ± 0.0007 |
NK | 1 | 0.9985 ± 0.0010 | 0.9998 ± 0.0004 |
SC | 1 | 0.9982 ± 0.0008 | 1.0000 ± 0.0008 |
SSIM | 1 | 0.9285 ± 0.0313 | 0.9523 ± 0.0290 |
DSC-Skull | DSC-Background | SVD-Skull | HD-Skull |
---|---|---|---|
0.8206 ± 0.080 | 0.9902 ± 0.0003 | 0.1794 ± 0.080 | 48.56 ± 03.69 |
0.8114 ± 0.005 | 0.9831 ± 0.0011 | 0.1886 ± 0.005 | 49.71 ± 06.21 |
0.8294 ± 0.012 | 0.9875 ± 0.0007 | 0.1706 ± 0.012 | 47.57 ± 08.61 |
0.8626 ± 0.016 | 0.9890 ± 0.0008 | 0.1374 ± 0.016 | 46.60 ± 07.76 |
0.8974 ± 0.011 | 0.9946 ± 0.0004 | 0.1026 ± 0.011 | 49.20 ± 10.86 |
0.8302 ± 0.011 | 0.9817 ± 0.0010 | 0.1698 ± 0.011 | 56.17 ± 07.55 |
0.7888 ± 0.010 | 0.9898 ± 0.0004 | 0.2112 ± 0.010 | 50.81 ± 09.57 |
0.8361 ± 0.014 | 0.9891 ± 0.0012 | 0.1639 ± 0.014 | 34.27 ± 14.06 |
0.8346 ± 0.033 | 0.9881 ± 0.0041 | 0.1654 ± 0.033 | 47.86 ± 06.21 |
Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations. |
© 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
Share and Cite
Dalvit Carvalho da Silva, R.; Jenkyn, T.R.; Carranza, V.A. Convolutional Neural Networks and Geometric Moments to Identify the Bilateral Symmetric Midplane in Facial Skeletons from CT Scans. Biology 2021, 10, 182. https://doi.org/10.3390/biology10030182
Dalvit Carvalho da Silva R, Jenkyn TR, Carranza VA. Convolutional Neural Networks and Geometric Moments to Identify the Bilateral Symmetric Midplane in Facial Skeletons from CT Scans. Biology. 2021; 10(3):182. https://doi.org/10.3390/biology10030182
Chicago/Turabian StyleDalvit Carvalho da Silva, Rodrigo, Thomas Richard Jenkyn, and Victor Alexander Carranza. 2021. "Convolutional Neural Networks and Geometric Moments to Identify the Bilateral Symmetric Midplane in Facial Skeletons from CT Scans" Biology 10, no. 3: 182. https://doi.org/10.3390/biology10030182
APA StyleDalvit Carvalho da Silva, R., Jenkyn, T. R., & Carranza, V. A. (2021). Convolutional Neural Networks and Geometric Moments to Identify the Bilateral Symmetric Midplane in Facial Skeletons from CT Scans. Biology, 10(3), 182. https://doi.org/10.3390/biology10030182