mstefano Support for the k-Wave MATLAB toolbox en-US Wed, 13 May 2026 12:04:57 +0000 http://bbpress.org/?v=1.0.2 q http://www.k-wave.org/forum/search.php http://www.k-wave.org/forum/topic/questions-about-transcranial-ultrasound-simulation#post-7091 Fri, 18 Oct 2019 20:15:20 +0000 Bradley Treeby 7091@http://www.k-wave.org/forum/ <p>Hi Robert,</p> <p>Yes, <code>kspaceFirstOrder2D</code> accounts for effects like refraction and reflection.</p> <p>If your simulation is at very high pressure, then nonlinear effects can become important near the focus. However, in many cases the interaction at the skull surface can be assumed to be linear. See <a href="https://doi.org/10.1121/1.5126685">this paper</a> for example.</p> <p>Brad. </p> http://www.k-wave.org/forum/topic/questions-about-transcranial-ultrasound-simulation#post-7065 Wed, 02 Oct 2019 07:11:47 +0000 Robert W 7065@http://www.k-wave.org/forum/ <p>Hi,I want to simulate transcranial transmission of ultrasound.Here the brain consist of two different types of tissues, which are general tissue(speed=1500,desity=1040,absorption coefficient=0.6) and bone(speed=3200,desity=1990,absorption coefficient=3.5).Can the following code simulate the ultrasound transmission in heterogeneous medium? Does the simulation conclude the refraction and reflection in the<br /> interface between bone and general tissue? Do I need to consider other factors for HIFU,like nonlinear effects? Thank you very much! </p> <p>%model is the 2D map of brain.The model with value larger than 150 is bone and the other tissue is general<br /> %tissue<br /> [Nx, Ny] = size(model); %Nx=128 and Ny=128<br /> dx = 1e-3; % grid point spacing in the x direction [m]<br /> dy = 1e-3; % grid point spacing in the y direction [m]<br /> kgrid = kWaveGrid(Nx, dx, Ny, dy);<br /> medium.sound_speed = 1500 * ones(Nx, Ny); %general tissue<br /> medium.sound_speed(model&gt;=150)=3200; % bone</p> <p>medium.density = 1000 * ones(Nx, Ny); % general tissue<br /> medium.density(model&gt;=150)=1990; % bone</p> <p>medium.alpha_power = 1.5; % default<br /> medium.alpha_coeff = 0.6 * ones(Nx, Ny); % general tissue<br /> medium.alpha_coeff(model&gt;=150)=3.5; % bone</p> <p>% create initial pressure distribution using makeDisc<br /> disc_magnitude = 5; % [Pa]<br /> disc_x_pos = 50; % [grid points]<br /> disc_y_pos = 50; % [grid points]<br /> disc_radius = 8; % [grid points]<br /> disc_1 = disc_magnitude * makeDisc(Nx, Ny, disc_x_pos, disc_y_pos, disc_radius);<br /> source.p0 = disc_1;</p> <p>% define a centered circular sensor<br /> sensor_radius = 5e-2; % [m]<br /> num_sensor_points = 50;<br /> sensor.mask = makeCartCircle(sensor_radius, num_sensor_points);</p> <p>%simulation<br /> sensor_data = kspaceFirstOrder2D(kgrid, medium, source, sensor); </p> http://www.k-wave.org/forum/topic/getting-started-with-mrict-scans-intracranial-pressure-maps-skull-aberration#post-6368 Thu, 22 Mar 2018 19:38:45 +0000 Hammerben1 6368@http://www.k-wave.org/forum/ <p>Thank you! </p> http://www.k-wave.org/forum/topic/getting-started-with-mrict-scans-intracranial-pressure-maps-skull-aberration#post-6361 Wed, 21 Mar 2018 21:36:36 +0000 Bradley Treeby 6361@http://www.k-wave.org/forum/ <p>Hi Ben,</p> <p>It should be straightforward. First load the CT data into MATLAB using an appropriate dicom or nifty reader. Assemble the data into a 3D matrix, then pass to the function. You will need to check that the Hounsfield Units in your dataset are scaled in the same way as expected by <code>hounsfield2density</code> (see <a href="http://www.k-wave.org/forum/topic/replace-the-phantom-with-a-3d-ct-volume#post-6268">this thread</a>).</p> <p>Brad. </p> http://www.k-wave.org/forum/topic/getting-started-with-mrict-scans-intracranial-pressure-maps-skull-aberration#post-6352 Tue, 20 Mar 2018 00:01:47 +0000 Hammerben1 6352@http://www.k-wave.org/forum/ <p>Hi Brad:<br /> This is exactly what we are trying to do as well.<br /> So basically we could use hounsfield2density to transfer a CT scan to a spatial profile of densities. Can you dig deeper into this topic? Exactly how would you do that?<br /> Is there an example for conversion CT scan to a spatial profile of skull density?<br /> Thank you so much in advance!</p> <p>Ben </p> http://www.k-wave.org/forum/topic/getting-started-with-mrict-scans-intracranial-pressure-maps-skull-aberration#post-6323 Wed, 07 Mar 2018 22:33:00 +0000 Bradley Treeby 6323@http://www.k-wave.org/forum/ <p>Hi Justin,</p> <p>You could import the skull geometry from a CT scan, and then either use <code>hounsfield2density</code>, or one of the conversion algorithms based on porosity reported in the literature, e.g., <a href="https://doi.org/10.1121/1.1529663">this paper</a>. If you use the <code>makeBowl</code> function to define your transducer, it should be straightforward to orient it in the desired direction. Regarding the wave amplitude, for neuromodulation, the wave propagation is linear, so the amplitude of the output will be proportional to the amplitude of the input. If you're trying to simulate an experimental setup, you calibrate the input amplitude using a hydrophone measurement.</p> <p>Hope that helps,</p> <p>Brad. </p> http://www.k-wave.org/forum/topic/getting-started-with-mrict-scans-intracranial-pressure-maps-skull-aberration#post-6308 Fri, 02 Mar 2018 17:47:06 +0000 jmfine 6308@http://www.k-wave.org/forum/ <p>I have a few questions to try and get started on a (potentially lofty) goal. At the moment, we are using single element transducers to do low frequency neuromodulation. Clearly the skull causes both attenuation and distortion of ultrasound (assumption is that gray/white matter soft tissue has neglect-able impact). I am (first) trying to both estimate the intracranial pressure map and extent of skull distortion of the beam for this single transducer setup. Then, I would like to be able to do the same for a 4 element phased array that will allow beam steering etc...<br /> In this paper (<a href="http://iopscience.iop.org/article/10.1088/1741-2552/aa843e/pdf" rel="nofollow">http://iopscience.iop.org/article/10.1088/1741-2552/aa843e/pdf</a>) they did something similar for the single transducer setup. </p> <p>How would I best get started to replicate that? Is this under the<br /> Heterogeneous Propagation Medium Example"? I have gone thru the example code already and ran it successfully and altered the transducer freq, etc.. Nonetheless, I am not sure how to program in the parameters (speed of sound, density, attenuation) for all of the layers (bone, etc). Furthermore, I am unsure what the appropriate initial pressure setting should be.</p> <p>Furthermore, how would I go about defining the grid such that the transducer source/face would be parallel to the skull at a desired point?</p> <p>Thank for taking the time to field these questions.<br /> An aside, this is all for neuroresearch at Arizona State. If you have the time to discuss more on phone/Gchat, we would be happy to collaborate on this (jmfine@asu.edu). </p> <p>The end game is to actually use the 4channel system, calculate the distortion, then correct for it with the phased array. </p> <p>Justin Fine, PhD. </p> http://www.k-wave.org/forum/topic/best-way-to-simulate-more-than-two-layered-materials-in-2d#post-5381 Thu, 11 Feb 2016 18:38:33 +0000 buagciar 5381@http://www.k-wave.org/forum/ <p>thank you!!!</p> <p>i can not figure this out, wokr for me! </p> http://www.k-wave.org/forum/topic/transition-from-sound-in-liquids-to-solids#post-5350 Fri, 18 Dec 2015 01:02:20 +0000 mavheart 5350@http://www.k-wave.org/forum/ <p>Hi Brad,</p> <p>thank you for your help :)</p> <p>Marvin </p> http://www.k-wave.org/forum/topic/transition-from-sound-in-liquids-to-solids#post-5339 Tue, 01 Dec 2015 11:31:52 +0000 Bradley Treeby 5339@http://www.k-wave.org/forum/ <p>Hi Marvin,</p> <p>It seems to be a plot scale issue. With auto plot scaling, the limits are constantly adjusted, so it looks like there are waves remnant in your grid after the pulse reaches the PML, even though these are very small.</p> <p>If you change your code to <code>&#39;PlotScale, [-1, 1]</code> it should work as expected. Also, I would advise using a slightly fatter PML (perhaps 20 grid points).</p> <p>Hope that helps,</p> <p>Brad. </p> http://www.k-wave.org/forum/topic/transition-from-sound-in-liquids-to-solids#post-5326 Tue, 24 Nov 2015 22:19:57 +0000 mavheart 5326@http://www.k-wave.org/forum/ <p>Hi Brad,</p> <p>the new version does not seem to solve the issue. I would be glad if you took a look at my code :)</p> <p>Best regards,<br /> Marvin</p> <p>clear all;</p> <p>DATA_CAST = 'double';<br /> MASK_PLANE = 'xy';<br /> USE_STATISTICS = true;</p> <p>PML_X_SIZE = 10;<br /> PML_Y_SIZE = 10;</p> <p>Nx = 100;<br /> Ny = 100;</p> <p>c_water = 1500; % [m/s]<br /> c_plastic = 2230; % [m/s]<br /> c_poly = 1560; % [m/s]<br /> c_air = 343; % [m/s] @ 20°C</p> <p>rho_water = 998; % [kg/m^3]<br /> rho_plastic = 1330; % [kg/m^3]<br /> rho_poly = 1100; % [kg/m^3]<br /> rho_air = 1.22; % [kg/m^3]</p> <p>freq = 15e3; % [Hz]</p> <p>lambda = c_water/freq;</p> <p>x = 1;</p> <p>dx = x/Nx; % [m]<br /> dy = dx; % [m]</p> <p>kgrid = makeGrid(Nx, dx, Ny, dy);</p> <p>tr_pos = [round(0.5*Nx), round(0.5*Ny)];<br /> tr_rad = 10.8e-2/(2);</p> <p>tr_pos_abs = [tr_pos(1)*dx, tr_pos(2)*dy]</p> <p>ITC = makeDisc(Nx, Ny, tr_pos(1), tr_pos(2), round(tr_rad/dx));</p> <p>medium.sound_speed_compression = c_water*ones(Nx, Ny);<br /> medium.sound_speed_shear = zeros(Nx, Ny);<br /> medium.density = rho_water*ones(Nx, Ny);</p> <p>t_end = 10e-4; % [s]</p> <p>kgrid.t_array = makeTime(kgrid, c_water*1.5);</p> <p>delta_t = kgrid.t_array(2) - kgrid.t_array(1);</p> <p>ncycles = 2;</p> <p>input_signal = toneBurst(1/delta_t, freq, ncycles);</p> <p>source.sxx = input_signal;<br /> source.syy = input_signal;</p> <p>source.s_mask = ITC;</p> <p>sensor.mask = zeros(Nx, Ny);<br /> sensor.mask(50, 100) = 1;</p> <p>input_args = {'PlotScale', 'auto','PMLSize', [PML_X_SIZE, PML_Y_SIZE],...<br /> 'DataCast', DATA_CAST, 'DataRecast', true,'PlotPML', true};</p> <p>sensor_data = pstdElastic2D(kgrid, medium, source, sensor, input_args{:}); </p> http://www.k-wave.org/forum/topic/transition-from-sound-in-liquids-to-solids#post-5321 Tue, 24 Nov 2015 15:20:50 +0000 Bradley Treeby 5321@http://www.k-wave.org/forum/ <p>Hi Marvin,</p> <p>That certainly sounds suspicious. If you post your code, I can take a look.</p> <p>Also, have you updated to k-Wave version 1.1.1? This corrected a bug in the <code>pstdElastic</code>codes that might affect stability. </p> <p>Brad. </p> http://www.k-wave.org/forum/topic/transition-from-sound-in-liquids-to-solids#post-5314 Tue, 17 Nov 2015 23:26:33 +0000 mavheart 5314@http://www.k-wave.org/forum/ <p>Hi Brad!</p> <p>Thank you for your reply. I used a test simulation in 2D to have a look at the behaviour of pstdElastic for liquids before applying it to more complex volumes and I encountered a problem:</p> <p>I put a stress source (disc) into a grid of water. Then I created a burst signal and applied it to the source like this:</p> <p>source.sxx = input_signal;<br /> source.syy = input_signal;</p> <p>It looked like it would work fine - I was trying to achieve homogenous radiation - but as the pressure waves reached the corners of my grid, everything inside the medium but the PML seemed to explode, reaching high pressure values. Is there a way to mess up your PML so that this happens? I tried turning it off and it was a completely different result.</p> <p>Thanks for your help!</p> <p>Marvin </p> http://www.k-wave.org/forum/topic/transition-from-sound-in-liquids-to-solids#post-5289 Fri, 23 Oct 2015 10:04:11 +0000 Bradley Treeby 5289@http://www.k-wave.org/forum/ <p>Hi Marvin,</p> <p>To do this, you can use the <code>pstdElastic</code> functions and set the shear properties in the fluid part of the domain to zero. There is an example of this included in the toolbox (see <a href="http://www.k-wave.org/documentation/example_ewp_layered_medium.php">here</a>).</p> <p>Brad. </p> http://www.k-wave.org/forum/topic/transition-from-sound-in-liquids-to-solids#post-5283 Thu, 22 Oct 2015 20:43:55 +0000 mavheart 5283@http://www.k-wave.org/forum/ <p>Hello!</p> <p>I'm interested in sound propagation from liquid to solid and vice versa.<br /> I understand the new functions pstdElastic are meant for solids while kSpaceFirstOrder is meant for liquids. Is there a way built in to have those simulations interact in a way that allows for pressure or stress waves to travel from one to the other?</p> <p>Thank you very much for this powerful toolbox!</p> <p>Marvin Willam </p> http://www.k-wave.org/forum/topic/best-way-to-simulate-more-than-two-layered-materials-in-2d#post-5195 Wed, 05 Aug 2015 18:18:26 +0000 MUMiles 5195@http://www.k-wave.org/forum/ <p>Solved!</p> <p>I was going about this wrong. The correct way is to define your grid and then use:</p> <p><code>medium.sound_speed_compression = medium.sound_speed_compression + 5000*makeDisc(Nx, Ny, Nx/2 ... etc</code> </p> http://www.k-wave.org/forum/topic/best-way-to-simulate-more-than-two-layered-materials-in-2d#post-5194 Wed, 05 Aug 2015 17:37:12 +0000 MUMiles 5194@http://www.k-wave.org/forum/ <p>Thanks Anthony, that did the trick! As far as using makeDisc I am still a little confused. I can populate my grid points for a material but when I try to define a disc in the center the plot just becomes "grayed out". Here is how I am trying to define different material parameters for a disc in the center:</p> <pre><code>medium.sound_speed_compression = 5000*makeDisc(Nx, Ny, Nx/2, Ny/2, 2, &#39;true&#39;); medium.sound_speed_shear = 2000*makeDisc(Nx, Ny, Nx/2, Ny/2, 2); medium.density = 6000*makeDisc(Nx, Ny, Nx/2, Ny/2, 2);</code></pre> http://www.k-wave.org/forum/topic/best-way-to-simulate-more-than-two-layered-materials-in-2d#post-5185 Fri, 31 Jul 2015 08:36:30 +0000 Anthony 5185@http://www.k-wave.org/forum/ <p>Hi MUMiles,</p> <p>First of all, you have a <code>3/Nx</code> instead of <code>Nx/3</code>. Then, if you look at the order of your material definition, the third one comprises (and though erases) the second one. Try <code>2*Nx/3</code>, and it will work ;-)</p> <p><code>makeDisc</code> will help you for the circles.</p> <p>Anthony </p> http://www.k-wave.org/forum/topic/best-way-to-simulate-more-than-two-layered-materials-in-2d#post-5183 Fri, 31 Jul 2015 00:28:51 +0000 MUMiles 5183@http://www.k-wave.org/forum/ <p>Hello, </p> <p>First off thank you so much for offering this package free of charge. I am trying to simulate more than two layers of elastic/viscoelastic materials and am running into a problem when coding more than two layers. Here is the general process I am using:</p> <blockquote><p> % Define properties of the first layer (FOAM)<br /> medium.sound_speed_compression = 2278*ones(Nx, Ny); % [m/s]<br /> medium.sound_speed_shear = 30*zeros(Nx, Ny); % [m/s]<br /> medium.density = 1265*ones(Nx, Ny); % [kg/m^3] </p> <p>% Define properties of the second layer (Steel)<br /> medium.sound_speed_compression(Nx/2:end, :) = 5164; % [m/s]<br /> medium.sound_speed_shear(Nx/2:end, :) = 2164; % [m/s]<br /> medium.density(Nx/2:end, :) = 7500; % [kg/m^3]</p> <p>% Define properties of the third layer (PMMA)<br /> medium.sound_speed_compression(3/Nx:end, :) = 11663; % [m/s]<br /> medium.sound_speed_shear(Nx/3:end, :) = 1663; % [m/s]<br /> medium.density(Nx/3:end, :) = 11185; % [kg/m^3]</p> <p>etc...</p> </blockquote> <p>But it seems as though I always end up with just two materials. Any insight into what I'm doing wrong is greatly appreciated. Also, it there a way to make the layers circular? Like if I wanted to take a cross section of a sphere in the center. My problem involves coated spheres. Thanks! </p> http://www.k-wave.org/forum/topic/acoustic-intensity#post-4450 Wed, 09 Apr 2014 20:53:01 +0000 qiangbo 4450@http://www.k-wave.org/forum/ <p>Thanks. It is a great explanation! </p>