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83 results for “functional Ultrasound”
Transmission ultrasound data simulated using the k-Wave toolbox as a benchmark for biomedical quantitative ultrasound tomography using a ray approximation to Green's function
<p><strong>Transmission ultrasound data simulated using the k-Wave toolbox as a benchmark for biomedical quantitative ultrasound tomography using a ray approximation to Green's function </strong></p> <p> </p> <p>The folder ‘’simulation<em>’’ </em>includes the transmission ultrasound data sets used in the project:<a href="https://github.com/Ash1362/ray-based-quantitative-ultrasound-tomography">https://github.com/Ash1362/ray-based-quantitative-ultrasound-tomography</a>. In the Github link, the associated project can be found in the branch master in the folder r-Wave #V1.1. (The folder ‘’data_ust_kWave_transmission.zip<em>’’ </em>is deprecated.)</p> <p>...........................................................................................</p> <p>The ultrasound data were simulated using the k-Wave toolbox (version 1.3.) [5] and using a digital breast phantom [4]. In k-Wave version 1.4., no changes have been reported that affects the simulations. The simulations were done assuming isotropic point sources.</p> <p>The folder ‘’simulation<em>’’ </em> must be added to the path:</p> <p><em>''…r-Wave/data/simulation/…''</em></p> <p>For running the Matlab example scripts in the project in the github, the user has two choices: </p> <ol> <li>Simulate the k-Wave ultrasound data by setting <em>data_sim=true;</em> in the examples in the project.</li> <li>Upload the already simulated k-Wave ultrasound data according to the description below and load them by setting <em>data_sim=false;</em> in the examples in the project.</li> </ol> <p>Please read the description in the example scripts!</p> <p>…………………………………………………………………………………</p> <p>The folder simulation includes 2 subfolders, ‘’phantom<em>’’ </em>and ‘’data_ust_kWave_transmission<em>’’.</em></p> <p>1) The subfolder ‘’simulation/phantom<em>’’ </em> includes ‘’OA-BREAST<em>’’. </em></p> <p>In the project: https://anastasio.bioengineering.illinois.edu/downloadable-content/oa-breast-database/,</p> <p>the user must upload the folder ‘’Neg_47_Left<em>’’ </em>, and add it as ‘’r-wave/data/simulation/phantom/OA-BREAST/Neg_47_Left/<em>’’.</em></p> <p><em>.......................................................................................................................................................................</em></p> <p>2) The subfolder ‘’simulation/data_ust_kWave_transmission’<em>’ </em>includes 2 subfolders, ‘’2D<em>’’ </em> and ‘’3D<em>’’ </em>.</p> <p>The subfolder ‘’2D<em>’’ </em> includes:</p> <p><strong>data_ust_kWave_transmission/2D/PulsePammoth_1_dx4_cfl1_Nr256_Ne64_Interpoffgrid_Transgeompoint_Absorption1_CodeMatlab/data4_sphere_nonsmooth.mat</strong></p> <p>Two transmission ultrasound data sets were simulated using the k-wave for only water and breast in water according to section <em>‘’6.1. data simulation’’</em> in [1]. 64 emitters and 256 receivers are simulated as off-grid points which are placed on a 2D circular ring. (The characters ‘’_sphere_’’ are added to indicate that the transducers are placed on a ring.) To simulate the data, each emitter was individually driven by an excitation pulse, and the induced acoustic pressure time series were recorded on all the receivers. The k-Wave simulation was performed on a grid with grid spacing 0.4 mm, and the time spacing was set using a CFL number 0.1. The acoustic absorption and dispersion were accounted for based on the frequency power law. This data set is used for the purpose of image reconstruction, and therefore, the sound speed and absorption coefficients maps are not smoothed, i.e., the original maps are used for simulations. This data set can be used for image reconstruction using the time-of-flight-based approach and then the Green's approach.</p> <p><strong>data_ust_kWave_transmission/2D/PulsePammoth_1_dx4_cfl1_Nr256_Ne64_Interpoffgrid_Transgeompoint_Absorption1_CodeMatlab/data4_plane_nonsmooth.mat</strong></p> <p>Two transmission ultrasound data sets were simulated using the k-wave for only water and breast in water. 64 emitters and 256 receivers are simulated as off-grid points which are placed on 16 planar arrays which are all aligned with a circle. Each planar array includes 4 emitters and 16 receivers. Therefore, in contrast with the data mentioned above, the ray linking is performed using the line equations defining the 2D geometry of the linear arrays. (The characters ‘’_plane_’’ are added to indicate that the transducers are placed on line.) To simulate the data, each emitter was individually driven by an excitation pulse, and the induced acoustic pressure time series were recorded on all the receivers. The k-Wave simulation was performed on a grid with grid spacing 0.4 mm, and the time spacing was set using a CFL number 0.1. The acoustic absorption and dispersion were accounted for based on the frequency power law. This data set is used for the purpose of image reconstruction, and therefore, the sound speed and absorption coefficients maps are not smoothed, i.e., the original maps are used for simulations. This data set can be used for image reconstruction using the time-of-flight-based approach, but ahs not been extended to the Green's approach yet. The image reconstruction should be slower than the circular array. the reason is for circular array, for each emitter, the raylinking problem is solved for all receivers once using the equation of circle. However, for this data set, for each emitter, the ray linking problem is solved for each receiver array separately, because receiver arrays are defined with different line equations.</p> <p><strong>data_ust_kWave_transmission/2D/PulsePammoth_1_dx4_cfl1_Nr256_Ne64_Interpoffgrid_Transgeompoint_Absorption1_CodeMatlab/data4_sphere_smooth_17_1.mat</strong></p> <p>Two transmission ultrasound data sets were simulated using the k-Wave for only water and breast in water as the benchmark for validation of ray approximation to Green’s function in homogeneous and heterogenous media, respectively. The simulation was performed according to section <em>‘’6.2. Numerical validation of the ray approximation to the Green’s function’’</em> in [1].</p> <p>64 emitters and 256 receivers are simulated as off-grid points which are placed on a 2D circular ring. (The characters ‘’_sphere_’’ are added to indicate that the transducers are placed on a ring.) The pressure field was produced by emitter 1 (of the 64 emitters) and was recorded in time on all 256 receivers. The k-Wave simulation was performed on a grid with grid spacing 0.4 mm, and the time spacing was set using a CFL number 0.1. The acoustic absorption and dispersion were accounted for based on the frequency power law. The sound speed and absorption coefficient maps were smoothed by an averaging window of size 17 grid points. This data set is used as the benchmark for measuring accuracy of ray approximation to Green’s function for computing phase and amplitude of the pressure field on the receivers.</p> <p><strong>data_ust_kWave_transmission/2D/PulsePammoth_1_dx4_cfl1_Nr256_Ne64_Interpoffgrid_Transgeompoint_Absorption1_CodeMatlab/data4_sphere_smooth_17_20.mat</strong></p> <p> This data set is the same as data4_smooth_17_1 except the pressure field is produced by emitter 20.</p> <p>………………………………………………………………………………………………………………….</p> <p>The subfolder ‘’3D<em>’’ </em> includes:</p> <p><strong>data_ust_kWave_transmission/3D/PulsePammoth_1_dx5_cfl1_Nr4096_Ne1024_Interpnearest_Transgeompoint_Absorption0_CodeCUDA/data5_sphere_nonsmooth_tof_singram.mat</strong></p> <p>The discrepancy of time-of-flight data for two transmission ultrasound data sets simulated by the k-wave for breast in water and only water according to section 5.2 in [3]. The pressure fields were produced by 1024 emitters separately and were recorded on 4096 receivers. The emitters and receivers were simulated as points which are placed on a 3D hemispherical surface, and are interpolated onto the grid using a neighboring interpolation. The k-Wave simulations were performed on a grid with grid spacing 0.5 mm, and the time spacing was set using a CFL number 0.1. The time-of-flight data were computed and will be used for a refraction-corrected image reconstruction of the sound speed based on the inversion approach proposed in [3].</p> <p><strong>References</strong></p> <p>1 - A. Javaherian, ❝Hessian-inversion-free ray-born inversion for high-resolution quantitative ultrasound tomography❞, 2022, <a href="https://arxiv.org/abs/2211.00316/">https://arxiv.org/abs/2211.00316/</a> .</p> <p>2 - A. Javaherian and B. Cox, ❝Ray-based inversion accounting for scattering for biomedical ultrasound tomography❞, Inverse Problems vol. 37, no.11, 115003, 2021. <a href="https://iopscience.iop.org/article/10.1088/1361-6420/ac28ed/">https://iopscience.iop.org/article/10.1088/1361-6420/ac28ed/</a></p> <p>3- A. Javaherian, F. Lucka and B. T. Cox, ❝Refraction-corrected ray-based inversion for three-dimensional ultrasound tomography of the breast❞, Inverse Problems, 36 125010. <a href="https://iopscience.iop.org/article/10.1088/1361-6420/abc0fc/">https://iopscience.iop.org/article/10.1088/1361-6420/abc0fc/</a> </p> <p>4- Y. Lou, W. Zhou, T. P. Matthews, C. M. Appleton and M. A. Anastasio, ❝Generation of anatomically realistic numerical phantoms for photoacoustic and ultrasonic breast imaging❞, J. Biomed. Opt., vol. 22, no. 4, pp. 041015, 2017. <a href="https://anastasio.bioengineering.illinois.edu/downloadable-content/oa-breast-database/">https://anastasio.bioengineering.illinois.edu/downloadable-content/oa-breast-database/</a></p> <p>5 - B. E. Treeby and B. T. Cox, ❝k-Wave: MATLAB toolbox for the simulation and reconstruction of photoacoustic wave fields❞, J. Biomed. Opt. vol. 15, no. 2, 021314, 2010. <a href="http://www.k-wave.org/">http://www.k-wave.org/</a></p>
Functional Ultrasound Localization Microscopy reveals brain-wide neurovascular activity on a microscopic scale
<p>Matlab script to process fULM dynamic maps and compute activation maps. Two dataset are provided : one from a whiskers stimulation experiment in rats and one from a visual stimulation experiment in rats.</p>
Data for: Ear pinnae in a neotropical katydid (Orthoptera: Tettigoniidae) function as ultrasound guides for bat detection
<p>Early predator detection is a key component of the predator-prey arms race and has driven the evolution of multiple animal hearing systems. Katydids (Insecta) have sophisticated ears, each consisting of paired tympana on each foreleg that receive sound both externally, through the air, and internally via a narrowing ear canal running through the leg from an acoustic spiracle on the thorax. These ears are pressure-time difference receivers capable of sensitive and accurate directional hearing across a wide frequency range. Many katydid species have cuticular pinnae which form cavities around the outer tympanal surfaces, but their function is unknown. We investigated pinnal function in the katydid Copiphora gorgonensis by combining experimental biophysics and numerical modelling using 3D ear geometries. We found that the pinnae in C. gorgonensis do not assist in directional hearing for conspecific call frequencies, but instead act as ultrasound detectors. Pinnae induced large sound pressure gains (20–30 dB) that enhanced sound detection at high ultrasonic frequencies (>60 kHz), matching the echolocation range of co-occurring insectivorous gleaning bats. These findings were supported by behavioural and neural audiograms and pinnal cavity resonances from live specimens, and comparisons with the pinnal mechanics of sympatric katydid species, which together suggest that katydid pinnae primarily evolved for the enhanced detection of predatory bats.</p>
Effects of Underwater Ultrasound Therapy on Hand Function and Quality of Life in Patients With Rheumatoid Arthritis
ClinicalTrials.gov study NCT02706028. IPD Sharing: NO. Countries: 1. Publications: 1.
Feasibility Study of Ultrasound-guided Functional Remodeling of Lower Extremity Superficial Venous Valve
ClinicalTrials.gov study NCT05914740. IPD Sharing: NO. Countries: 1. Publications: 2.
Ultrasound and Functional Thyroid Evaluation
ClinicalTrials.gov study NCT04208503. IPD Sharing: YES. Countries: 1. Publications: 10.
Evaluation of the Functional Outcomes After Bilateral, 3D Ultrasound-guided Focal Thermal Ablation of the Prostate Transition Zone, in Patients with Benign Prostatic Hyperplasia-related Obstruction
ClinicalTrials.gov study NCT06212453. IPD Sharing: NO. Countries: 1. Publications: 6.
Synergic Effects of Ultrasound and Laser on the Pain Relief and Functionality
ClinicalTrials.gov study NCT02154893. IPD Sharing: Not stated. Countries: 1. Publications: 5.
The Effect of Ultrasound-Guided Erector Spinae Block on Respiratory Function After Laparoscopic Cholecystectomy
ClinicalTrials.gov study NCT03815799. IPD Sharing: NO. Countries: 1. Publications: 3.
Ultrasound and Psychobiological Correlates of Female Sexual Function
ClinicalTrials.gov study NCT02372643. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Point of Care Ultrasound to Evaluate Diaphragmatic Function in Children Undergoing Thoracic Surgery
ClinicalTrials.gov study NCT04400370. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Impact of Diabetic Polyneuropathy on Carpal Tunnel Syndrome: Shear Wave Elastography, Ultrasound, and Hand Function
ClinicalTrials.gov study NCT06933511. IPD Sharing: Not stated. Countries: 1. Publications: 5.
Ultrasound Duration Effects on Knee Osteoarthritis Pain and Function
ClinicalTrials.gov study NCT07057869. IPD Sharing: NO. Countries: 1. Publications: 5.
Functional Results of Infiltration for Biceps Tendonitis Guided by Ultrasound vs Anatomical Repairs: Variation in Technique
ClinicalTrials.gov study NCT06856824. IPD Sharing: NO. Countries: 1. Publications: 12.
Effect of Low-Intensity Pulsed Ultrasound on Functional Treatment of Class II Malocclusion
ClinicalTrials.gov study NCT03251807. IPD Sharing: NO. Countries: 1. Publications: 6.
Correlation Pelvic Floor Function and Ultrasound Findings One Year After Childbirth
ClinicalTrials.gov study NCT05530681. IPD Sharing: NO. Countries: 1. Publications: 33.
The Effect of Functional Task Training Combined With Therapeutic Ultrasound on Adults With Hip Osteoarthritis
ClinicalTrials.gov study NCT02798900. IPD Sharing: UNDECIDED. Countries: 1. Publications: 43.
Using Ultrasound to Study Respiratory Muscle Function in Critically Ill Patients
ClinicalTrials.gov study NCT03139695. IPD Sharing: NO. Countries: 1. Publications: 8.
Comparison of Two Exercise Training Modes on Left Myocardial Regional Function After Myocardial Infarction Evaluated by 2D Strain Ultrasound
ClinicalTrials.gov study NCT04190394. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Intraoperative Functional Ultrasound
ClinicalTrials.gov study NCT02656407. IPD Sharing: NO. Countries: 1. Publications: 2.
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