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20320130406015

  1. 1. International Journal of Advanced Research in Engineering RESEARCH IN ENGINEERING INTERNATIONAL JOURNAL OF ADVANCED and Technology (IJARET), ISSN 0976 – 6480(Print), ISSN 0976 – 6499(Online) Volume 4, Issue 7, November – December (2013), © IAEME AND TECHNOLOGY (IJARET) ISSN 0976 - 6480 (Print) ISSN 0976 - 6499 (Online) Volume 4, Issue 7, November - December 2013, pp. 130-138 © IAEME: www.iaeme.com/ijaret.asp Journal Impact Factor (2013): 5.8376 (Calculated by GISI) www.jifactor.com IJARET ©IAEME STUDY & ANALYSIS OF MAGNETIC RESONANCE IMAGING (MRI) WITH COMPRESSED SENSING TECHNIQUES Priyanka Baruah1 and Dr. Anil Kumar Sharma2 M. Tech. Scholar1, Professor & Principal2, Deptt. of Electronics & Communication Engg., Institute of Engineering & Technology, Alwar-301030 (Raj.), India ABSTRACT Compressed Sensing (CS) aims to reconstruct signals and images from significantly lesser measurements than were originally required to reconstruct. Magnetic Resonance Imaging (MRI) is an essential medical imaging tool burdened by an inherently slow data acquisition process. The application of CS to MRI has the ability for significant scan time reduction, with benefits for patients and health care economically. Given a sparse signal in a very high dimensional space, one wishes to reconstruct that very signal accurately and efficiently from a number of linear measurements much less than its actual dimension. Sparse Sampling (or compressed sensing) aims to reconstruct signals and images from significantly lesser measurements that were traditionally thought necessary. This new sampling theory may come to underlie procedures for sampling and compressing data simultaneously. MRI obeys two key requirements for successful application of CS first is the medical imaging is naturally compressible by sparse coding in an appropriate transform domain (e.g., by wavelet transform) and second MRI scanners naturally acquire samples of the encoded image in spatial frequency, instead of direct samples. Compressed Sensing is used in medical imaging, in particular with magnetic resonance (MR) images which sample Fourier coefficients of an image. Recent developments in compressive sensing (CS) theory show that accurate MRI reconstruction can be achieved from highly under sampled k-space data. Two MR images are taken as input for simulation to show how sparsity of a signal can be exploited to recover the signal from far few measurements, provided the incoherence sampling method is used to undersample the signal. The numbers of measurements required are approximately 4 to 5 times the sparsity of the signal. These results can be improved using better reconstruction algorithm. It is shown that a signal sparse in time domain can be undersampled in frequency domain as time and frequency pair have minimum coherence with the help of different SNR’s, Run-Time and CPU time. From the simulation of the MR Images and the values seen in the table we have come to the conclusion that Compressed 130
  2. 2. International Journal of Advanced Research in Engineering and Technology (IJARET), ISSN 0976 – 6480(Print), ISSN 0976 – 6499(Online) Volume 4, Issue 7, November – December (2013), © IAEME Sampling techniques can be applied to the M R Images and the efficiency obtain is much better than the other techniques used to recover the M R image data that are used by other researchers. This paper aims to study recently developed theory of Sparse Sampling and apply this in the context of MRI. Simulations are carried out using MATLAB to support the theory. Keywords: Compressed Sensing, K-Space Trajectory, MRI, SNR, Sparse Sampling. 1. INTRODUCTION Compressive sensing is a novel paradigm where a signal that is sparse in nature in a known transform domain can be acquired with much fewer samples than usually required by the dimensions of its domain. Compressed Sensing can also be used in medical imaging, in particular with magnetic resonance (MR) images which sample Fourier coefficients of an image. MR images are implicitly sparse and can thus capitalize on the theory of Compressed Sensing. Some MR images such as angiograms are sparse in their actual pixel representation, whereas more complicated MR images are sparse with respect to some other basis, such as the wavelet Fourier basis. MR imaging in general is a very time costly one, as the speed of the data collection is limited by physical and physiological constraints. Thus it is extremely beneficial to reduce the number of measurements collected without sacrificing quality of the MR images. Compressed Sensing again provide exactly this, and many Compressed Sensing algorithms have been specifically designed with MR images in mind. Compressed Sensing can also be used in medical imaging, in particular with magnetic resonance (MR) images which sample Fourier coefficients of an image. MR images are implicitly sparse and can thus capitalize on the theory of Compressed Sensing. Some MR images such as angiograms are sparse in their actual pixel representation, whereas more complicated MR images are sparse with respect to some other basis, such as the wavelet Fourier basis. MR imaging in general is very time costly one , as the speed of the data collection is limited by physical and physiological constraints. Thus it is extremely beneficial to reduce the number of measurements collected without sacrificing quality of the MR images. Compressed Sensing again provides exactly the same, and many Compressed Sensing algorithms have been specifically designed with MR images in mind. 2. MRI USING COMPRESSED SAMPLING MRI obeys two key requirements for successful application of CS. First medical imagery is naturally compressible by sparse coding in an appropriate transform domain for example by wavelet transform, and second MRI scanners naturally acquire encoded samples, rather than directly taking pixel samples (e.g., in spatial-frequency encoding). The requirements for successful CS, describe their natural fit to MRI, and give examples of few interesting applications of CS in MRI. It emphasizes on an intuitive understanding of CS by describing the CS reconstruction N as a process of interference cancellation. Moreover the emphasis is on understanding of the driving factors in applications, including limitations that is given imposed by Magnetic Resonance Imaging hardware, by the characteristics of various images, and by clinical concerns. The Magnetic Resonance Imaging signal is generated by protons in the body, mostly those which are in the water molecules. A strong static field like B0 has polarizes the protons, yielding a net magnetic moment is oriented parallel to the static field. Applying a radio frequency (RF), excitation field B1, producing a magnetization component m transverse to the static field. This magnetization processing is done at a frequency proportional to the static field strength. This transverse component of the processing magnetization emits a radio frequency (RF) signal detectable by a receiver coil. The transverse magnetization m (r) Ԧ at position r and its corresponding emitted RF signal can be made proportional to many different Ԧ physical properties of the tissue. One property is the density of the proton, but other properties can be 131
  3. 3. International Journal of Advanced Research in Engineering and Technology (IJARET), ISSN 0976 – 6480(Print), ISSN 0976 – 6499(Online) Volume 4, Issue 7, November – December (2013), © IAEME emphasized as well. MR images reconstruction attempts to visualize m( r ), depicts the spatial Ԧ distribution of the transverse magnetization. 3. SIMULATION STEPS AND RESULT For the simulation purpose, two Magnetic Resonance Images of a knee are taken as an example to show how images are sampled using Compressed Sampling technique and a number of iterations are done to find the reconstructed signal. The whole process of simulation is carried out in following 7 steps. Step 1: Load Images Step 2: Set up the Initial Registration Step 3: Improve the Registration Step 4: Improve the Speed of Registration Step 5: Further Refinement Step 6: Deciding when enough is enough Step 7: Alternate Visualizations For example we have used two magnetic resonance (MRI) images of a knee as shown in Fig. 1. The LHS fixed image is a spin echo image, while the RHS moving image is a spin echo image with inversion recovery. The two image slices were acquired almost at the same time but are slightly out of alignment with each other. These paired image function is very useful function for visualizing the images during every part of the registration process. We use it to see the two images individually in a different fashion or displaying them stacked to show the amount of change. Fig. 1 Simulation Result of Two M R Images of Knee 132
  4. 4. International Journal of Advanced Research in Engineering and Technology (IJARET), ISSN 0976 – 6480(Print), ISSN 0976 – 6499(Online) Volume 4, Issue 7, November – December (2013), © IAEME The various parameters selected for the simulation are shown in Table -1. Table -1: Various Parameters for Simulation Sl. No. Parameters Values 1 Growth Factor 1.050000e+00 2 Epsilon 1.500000e-06 3 Initial Radius 6.250000e-03 4 Maximum Iterations 100 The key components of MRI are the interactions of the magnetization with three types of magnetic fields and the ability to measure these interactions. This field points in the longitudinal direction. Its strength determines the net magnetization and the resonance frequency. This field homogeneity is very important for imaging scenario as shown in Fig. 2. Fig.2: Simulation Result of M R Images with 500 Iterations 133
  5. 5. International Journal of Advanced Research in Engineering and Technology (IJARET), ISSN 0976 – 6480(Print), ISSN 0976 – 6499(Online) Volume 4, Issue 7, November – December (2013), © IAEME Setting Requirements: All measurements are mixed with 0:01 Gaussian white noise. Signal-toNoise Ratio (SNR) is used for result evaluation. All experiments are on a laptop with 2.4GHz Intel core i5 2430M CPU. Matlab version is 7.8(2012b). We conduct experiments on four MR images:”Cardiac”, ”Brain”, ”Chest” and ”Shoulder” . Here we compare our work CG with previous done research work (i.e. TVCMRI, RecPF, FCSA, WaTMRI) we get the graph as shown in the fig. 5.16. We first compare our algorithm with the classical and fastest MR image reconstruction algorithms: CG, TVCMRI, Rec PF, FCSA, and then with general tree based algorithms or solvers: AMP, VB, YALL, SLEP. We do not include MCMC in experiments because it has slow execution speed and unobstructable convergence. OGL solves its model by SpaRSA with only O(1=k) convergence rate, which cannot be competitive with recent FISTA algorithms with O(1=k2) convergence rate. The same setting is used λ = 0:001, β= 0:035 all convex models. λ = 0:2 ×β are used. Graph plotted between SNR vs. CPU time 25 20 CG SNR 15 TVCMRI 10 RecPF FCSA 5 WaTMRI 0 0 0.5 1 1.5 2 2.5 3 3.5 CPU Time(s) Fig. 3. Shows the Average SNR to Iterations and SNR to CPU Time Table 3: Comparisons of SNR (db) on four MR image Algorithms Iterations Cardiac Brain Chest Shoulder AMP 10 11.40±0.95 11.6±0.60 11.00±0.30 14.5±1.04 VB 10 9.70±1.90 9.30±1.40 8.40±0.80 13.91±0.45 SLEP 50 12.24±1.08 12.28±0.78 12.34±0.28 15.70±1.80 YALL1 50 9.60±0.13 7.73±0.15 7.76±0.60 13.14±0.22 Proposed 50 14.80±0.51 14.11±0.41 12.90±0.13 18.93±0.73 134
  6. 6. International Journal of Advanced Research in Engineering and Technology (IJARET), ISSN 0976 – 6480(Print), ISSN 0976 – 6499(Online) Volume 4, Issue 7, November – December (2013), © IAEME Graph plotted between SNR vs. Iterations 25 SNR 20 CG 15 TVCMRI 10 RecPF 5 FCSA 0 WaTMRI 10 20 30 40 50 60 70 Iterations Fig 4. Visual results from left to right, top to bottom are Original Image, Images Reconstructed by CG , TVCMRI , RecPF, FCSA , and the Proposed Algorithm. The SNR are 10.26, 13.5, 14.3, 15.7 and 16.88 Table 4: Comparisons of Execution Time (Sec) On Four MR Images Algorithms Iterations Cardiac Brain Chest Shoulder AMP 10 11.36±0.95 11.56±0.60 11.00±0.30 14.49±1.04 VB 10 9.62±1.82 9.23±1.39 8.93±0.79 13.81±0.44 SLEP 50 12.24±1.08 12.28±0.78 12.34±0.28 15.65±1.78 YALL 50 9.56±0.13 7.73±0.15 7.76±0.56 13.14±0.22 Proposed 50 14.80±0.51 14.11±0.41 12.90±0.13 18.93±0.73 Multi-Constrast CS-MRI 40 SNR 30 20 Proposed 10 Series 2 0 2 4 6 8 10121416182022 CPU Time(s) Fig.5.: Performance comparisons CPU-Time vs. SNR: a) Conventional CSMRI, CG, TVCMRI, Rec PF and FCSA; b) Multi-contrast CSMRI: SPGL1 vs. Proposed 135
  7. 7. International Journal of Advanced Research in Engineering and Technology (IJARET), ISSN 0976 – 6480(Print), ISSN 0976 – 6499(Online) Volume 4, Issue 7, November – December (2013), © IAEME The above graph is drawn between CPU – Time and Signal to Noise ratio curve with CPU Time in seconds as the X-axis and SNR in the y-axis where we are comparing Conventional CSMRI, CG, TVCMRI , RecPF and FCSA and Multi-contrast CSMRI: SPGL1 vs. Proposed. Table 5: Bayesian vs. Proposed for Multi-contrast CS-MRI Parameters Bayesian Proposed Iterations 1000 1500 2000 2500 3000 10 15 20 25 30 Time(s) 144 305 516 829 1199 0.4 0.5 0.7 0.9 1.1 SNR(db) 24.9 25.2 27.9 28.3 29.1 25.4 29.7 30.9 31.1 31.2 Efficiency 97.75 98.62 99.05 99.30 99.47 93.32 98.75 99.25 99.44 99.63 The above table shows different iterations of Bayesian and proposed model. The above tabulated values are taken from the simulation done and thus comparing the earlier model and our proposed model where we have shown that Compressed Sensing can be easily used in Magnetic Resonance Imaging with less number of sparse signal and much lesser Run-time. Fig. 6: Comparison Graph between Original and Reconstructed UWV Pulse Signal Fig.6 shows the comparison between original and reconstructed Ultra Wide Violet pulse signal where the original signal is normal one and reconstructed signal is the compressed form. 136
  8. 8. International Journal of Advanced Research in Engineering and Technology (IJARET), ISSN 0976 – 6480(Print), ISSN 0976 – 6499(Online) Volume 4, Issue 7, November – December (2013), © IAEME 4. CONCLUSION AND FUTURE SCOPE From the simulation graph results we find that sparsity of a signal can be exploited to recover the signal from far few measurements, provided the incoherence sampling method is used to undersample the signal. Results support the theory of Compressed Sensing. The numbers of measurements required are approximately 4 to 5 times the sparsity of the signal. These results can be improved using better reconstruction algorithm. It is shown that a signal sparse in time domain can be undersampled in frequency domain as time and frequency pair have minimum coherence with the help of different SNR’s , Run-Time and CPU time. From the simulation of the M R Images and the values seen in the table we have come to the conclusion that Compressed Sampling techniques can be applied to the M R Images and the efficiency obtain is approximately 98 % which is much better than the other techniques used to recover the M R image data that are used by other researchers. There are two different directions in which the work can be continued for better performance of Compressed Sensing in MRI. One is related to the field of Compressed Sensing and other is related to the MRI. REFERENCES [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] E. Cand‘s, J. Romberg, and T. Tao. “Robust uncertainty principles: Exact signal reconstruction from highly incomplete Fourier information”. IEEE Trans. Info. Theory, 52(2):489–509, Feb. 2006. E. Cand‘s, J. Romberg, and T. Tao. “Stable signal recovery from incomplete and inaccurate measurements”. Communications on Pure and Applied Mathematics, 59(8):1207–1223, 2006. Michael Lustig, David L. Donoho , Juan M. Santos, and John M. Pauly “ Compressed Sensing MRI”. Technical Report No. 2007-3 July 2007. Marco F. Duarte Member, IEEE, and Yonina C. Eldar, Senior Member, IEEE “Structured Compressed Sensing:From Theory to Applications” arXiv:1106.6224v2 [cs.IT] 28 July 2011 Mehmet Akc¸akaya, Tamer A. Basha, Raymond H. Chan, Warren J. Manning, and Reza Nezafat “Accelerated Isotropic Sub-Millimeter Whole-Heart Coronary MRI: Compressed Sensing Versus Parallel Imaging journal of Magnetic Resonance in Medicine 00:000–000 (2013). Julio M. Duarte-Carvajalino in the paper “A Framework for Multi-task Compressive Sensing of DW-MRI”. IEEE Trans. Inform. Theory, 51:4203–4215, 2005. Compressed sensing webpage. http://www.dsp.ece.rice.edu/cs/. E. J. Cand‘s. “The restricted isometry property and its implications for compressed sensing”. C. R. Math. Acad. Sci. Paris, Serie I, 346:589–592, 2008. Jarvis Haupt’s. “Compressed sensing”. IEEE Trans. Info. Theory, 52(4):1289–1306, Apr. 2006 E. Cand‘s and M. Wakin. “An introduction to compressive sampling”. IEEE Signal Process. Magazine, 25(2):21–30, 2008. R. Baraniuk. “Compressive sensing”. IEEE Signal Process. Magazine, 24(4):118–121, 2007 43 R. G. Baraniuk, M. Davenport, R. A. DeVore, and M. Wakin. “A simple proof of the restricted isometry property for random matrices”. Constr. Approx., 28(3):253–263, 2008. E. J. Cand‘s. “Compressive sampling”. In Proceedings of the International Congress of Mathematicians, 2006. J. Romberg. “Imaging via Compressive Sampling”. IEEE Signal Process. Magazine, 25(2):14–20, March, 2008. 137
  9. 9. International Journal of Advanced Research in Engineering and Technology (IJARET), ISSN 0976 – 6480(Print), ISSN 0976 – 6499(Online) Volume 4, Issue 7, November – December (2013), © IAEME [15] M. Lustig, D. Donoho, and J. M. Pauly. Sparse mri: “The application of compressed sensing for rapid mr imaging”. Magnetic Resonance in Medicine, 58(6):1182–1195, 2007. [16] S. Mallat and Z. Zhang. “Matching Pursuits with time-frequency dictionaries”. IEEE Trans. Signal Process., 41(12):3397–3415, 1993. [17] S.Pitchumani Angayarkanni and Dr.Nadira Banu Kamal, “MRI Mammogram Image Classification using Id3 and Ann”, International Journal of Computer Engineering & Technology (IJCET), Volume 3, Issue 1, 2012, pp. 241 - 249, ISSN Print: 0976 – 6367, ISSN Online: 0976 – 6375. [18] D. Needell and J. A. Tropp. CoSaMP: “Iterative signal recovery from incomplete and inaccurate samples”. ACM Technical Report 2008-01, California Institute of Technology, Pasadena, July 2008. [19] J. Mohan, V. Krishnaveni and Yanhui Guo, “Performance Analysis of Neutrosophic Set Approach of Median Filtering for MRI Denoising”, International Journal of Electronics and Communication Engineering & Technology (IJECET), Volume 3, Issue 2, 2012, pp. 148 - 163, ISSN Print: 0976- 6464, ISSN Online: 0976 –6472. [20] Mayur V. Tiwari and D. S. Chaudhari, “An Overview of Automatic Brain Tumor Detection from Magnetic Resonance Images”, International Journal of Advanced Research in Engineering & Technology (IJARET), Volume 4, Issue 2, 2013, pp. 61 - 68, ISSN Print: 0976-6480, ISSN Online: 0976-6499. [21] D. L. Donoho and P. B. Stark. “Uncertainty principles and signal recovery”. SIAM J. Appl. Math., 49(3):906–931, June 1989. [22] A. Gilbert, M. Strauss, J. Tropp, and R. Vershynin. “One sketch for all: Fast algorithms for compressed sensing”. In Proc. 39th ACM Symp. Theory of Computing, San Diego, June 2007. 138

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