quetaijiangchu Support for the k-Wave MATLAB toolbox en-US Tue, 12 May 2026 23:09:02 +0000 http://bbpress.org/?v=1.0.2 q http://www.k-wave.org/forum/search.php http://www.k-wave.org/forum/topic/alpha-version-of-kwavearray-off-grid-sources/page/2#post-8873 Fri, 28 Jul 2023 10:50:03 +0000 nhaidour 8873@http://www.k-wave.org/forum/ <p>Hi Bradley,</p> <p>I'm simulating a disc element using karray.addDiscElement, but when I draw the 3D plot of this element, it seems the shape of the element is not a disc, it looks like it's rectangle, is this normal?</p> <p>Cordially, </p> http://www.k-wave.org/forum/topic/simulating-ultrasound-stimulation-in-the-human-brain#post-8856 Sat, 01 Jul 2023 10:47:06 +0000 quetaijiangchu 8856@http://www.k-wave.org/forum/ <p>Can share this file if allowed('final_tissues.nii.gz')？ </p> http://www.k-wave.org/forum/topic/alpha-version-of-kwavearray-off-grid-sources/page/2#post-8778 Tue, 30 May 2023 02:15:16 +0000 Jinhyuk Kim 8778@http://www.k-wave.org/forum/ <p>Thanks, Bradley!</p> <p>I have to adjust the position of the ultrasound transducer, right?</p> <p>I'll try and research successfully! </p> http://www.k-wave.org/forum/topic/alpha-version-of-kwavearray-off-grid-sources/page/2#post-8761 Thu, 18 May 2023 06:25:54 +0000 Bradley Treeby 8761@http://www.k-wave.org/forum/ <p>Hi Jinhyuk Kim,</p> <p>In <code>kWaveArray</code>, the element positions must be set in physical space (not grid space). So, in your example, there are no elements within the grid, so the mask ends up being zero (hence the error message).</p> <p>Brad </p> http://www.k-wave.org/forum/topic/alpha-version-of-kwavearray-off-grid-sources/page/2#post-8746 Thu, 27 Apr 2023 10:02:31 +0000 Jinhyuk Kim 8746@http://www.k-wave.org/forum/ <p>Hi everyone,</p> <p>I have a problem with the kspaceFirstOrder2D.</p> <p>error message is 'source.p_mask must be a binary grid with at least one element set to 1.</p> <p>I want to find acoustic fiend arising from array used kwavearray class, however, I found above error messasge.</p> <p>Here is my code.</p> <p>karray = kWaveArray;<br /> % define the grid parameters<br /> pml_size = 20;<br /> Nx = 552 - 2 * pml_size; % [grid points]<br /> Ny = 552 - 2 * pml_size; % [grid points]<br /> dx = 1e-3; % [m]<br /> dy = 1e-3; % [m]</p> <p>% create the computational grid<br /> kgrid = kWaveGrid(Nx, dx, Ny, dy);</p> <p>%% ALPHA COEFF</p> <p>medium.alpha_coeff = 0.02 * ones(Nx, Ny); % [dB/(MHz^y cm)] WATER<br /> medium.alpha_power = 1.5;</p> <p>%% SPEED<br /> medium.sound_speed = 1500 * ones(Nx, Ny); % WATER default fill! [m/s]<br /> % %skull</p> <p>%% DENSITY</p> <p>medium.density = 1000 * ones(Nx, Ny); % WATER default fill [kg/m^3]</p> <p>freq = 200*10^3; % [Hz]<br /> amp = 0.3e6; % 0.53[MPa]</p> <p>radius = 10e-3; % [m]<br /> diameter = 15e-3; % [m]<br /> focus_pos = [Nx/2, Ny/2]; % [m]</p> <p>% add arc shaped element<br /> elem_pos = [Nx/10, Ny/2]; % [m]<br /> karray.addArcElement(elem_pos, radius, diameter, focus_pos);</p> <p>% add arc shaped element<br /> elem_pos = [Nx/10, Ny/2.5]; % [m]<br /> karray.addArcElement(elem_pos, radius, diameter, focus_pos);</p> <p>% add arc shaped element<br /> elem_pos = [Nx/10, Ny/3.0]; % [m]<br /> karray.addArcElement(elem_pos, radius, diameter, focus_pos);</p> <p>source.p_mask = karray.getArrayBinaryMask(kgrid);</p> <p>display_mask = source.p_mask;</p> <p>% calculate the time step using an integer number of points per period<br /> ppw = 100; % points per wavelength<br /> cfl = 0.1; % cfl number<br /> ppp = 41; % points per period<br /> T = 1 / freq; % period [s]<br /> dt = 4e-8; % time step [s]</p> <p>% calculate the number of time steps to reach steady state<br /> t_end = 40.0575e-5;<br /> Nt = round(t_end / dt);</p> <p>% create the time array<br /> kgrid.setTime(Nt, dt);</p> <p>% define the input signal</p> <p>source.p = createCWSignals(kgrid.t_array, freq, [amp, amp, amp], 0);</p> <p>sensor.mask = ones(Nx, Ny);<br /> sensor.record = {'p', 'p_max_all'};</p> <p>% record the last 3 cycles in steady state<br /> num_periods = 15;<br /> T_points = round(num_periods * T ./ kgrid.dt);<br /> sensor.record_start_index = Nt - T_points + 1;</p> <p>% set the input arguements<br /> input_args = {'PMLInside', false,'PlotLayout', true, 'PlotPML', false, 'DisplayMask', display_mask, 'PlotScale', [-1, 1] * amp};</p> <p>% run the acoustic simulation<br /> sensor_data = kspaceFirstOrder2D(kgrid, medium, source, sensor, input_args{:});</p> <p>Thanks </p> http://www.k-wave.org/forum/topic/alpha-version-of-kwavearray-off-grid-sources/page/2#post-8745 Fri, 21 Apr 2023 06:03:48 +0000 zengqw2021 8745@http://www.k-wave.org/forum/ <p>Hi everyone,</p> <p> Is there a way for me to get grid points form part of the specified element. As for example_at_array_as_sensor.m, I got a sensor_data array of size 6748 by 1207. There is 20 elements.<br /> But, how could I tell which transducer these 6748 time series belong to.</p> <p> I find a property named 'getElementBinaryMask' may be work. But when I run it in the following way, I get an error 'Method, attribute, or field 'getElementBinaryMask' of class 'kWaveArray' not recognized.'.</p> <p>mask2 = karray.getElementBinaryMask(kgrid, 1); % grid points form part of the specified element</p> <p>Does anyone know how to solve this problem？ </p> http://www.k-wave.org/forum/topic/simulating-ultrasound-stimulation-in-the-human-brain#post-8686 Tue, 13 Dec 2022 05:00:53 +0000 sky 8686@http://www.k-wave.org/forum/ <p>You can give me that file ('final_tissues.nii.gz'), and how do you run load_nii </p> http://www.k-wave.org/forum/topic/simulating-ultrasound-stimulation-in-the-human-brain#post-8682 Thu, 01 Dec 2022 14:43:24 +0000 yichen 8682@http://www.k-wave.org/forum/ <p>Thank you Treeby! Your advice helps a lot! </p> http://www.k-wave.org/forum/topic/simulating-ultrasound-stimulation-in-the-human-brain#post-8681 Wed, 30 Nov 2022 21:35:09 +0000 Bradley Treeby 8681@http://www.k-wave.org/forum/ <p>Broadly speaking, that sounds right. See <a href="//www.k-wave.org/documentation/makeBowl.php”">the docs</a>. </p> http://www.k-wave.org/forum/topic/simulating-ultrasound-stimulation-in-the-human-brain#post-8680 Wed, 30 Nov 2022 08:48:18 +0000 yichen 8680@http://www.k-wave.org/forum/ <p>Thank you Treeby. I think it's the issue of CFL setting resulting in instability.</p> <p>After I reduced the CFL from 0.3 to 0.2, the simulation became reasonable.</p> <p>I have one more question regarding the setting of the ultrasound focus. I used makeBowl to generate an ultrasound transducer, which required several parameters to define the transducer. In the code below, could you please kindly check if I have set each parameter properly, as to what these parameters actually stand for?</p> <p>%% define the transducer<br /> radius = round(64e-3/dx); %transducer curvature in grid step<br /> diameter = round(64e-3/dx)+1; %transducer diameter in grid step<br /> pos_transducer = [96, 170 ,211]; %where to put the transducer<br /> focus_transducer = [96, 148, 167]; %where the ultrasound to be focused<br /> source.p_mask = makeBowl([Nx, Ny, Nz], pos_transducer, ...<br /> radius, diameter, focus_transducer, 'Plot', false);</p> <p>To my understanding, the input 'radius' and 'diameter' to the 'makeBowl' function stand for the physical property of the transducer, so these two parameters should be fixed regarding one specific transducer.<br /> As to the 'pos_transducer', it refers to the coordinate of the center of the transducer.<br /> As to the 'focus_transducer', it refers to the coordinate of the brain region we are intended to stimulate.</p> <p>Thanks again for your assistance! </p> http://www.k-wave.org/forum/topic/simulating-ultrasound-stimulation-in-the-human-brain#post-8679 Wed, 30 Nov 2022 05:30:16 +0000 yichen 8679@http://www.k-wave.org/forum/ <p>Thanks for your reply. I'll try with reducing CFL and get back to you later. </p> http://www.k-wave.org/forum/topic/simulating-ultrasound-stimulation-in-the-human-brain#post-8678 Tue, 29 Nov 2022 22:43:29 +0000 Bradley Treeby 8678@http://www.k-wave.org/forum/ <p>I haven't run your simulation, but it looks a lot like classic instability. Does it work if you reduce the CFL? </p> http://www.k-wave.org/forum/topic/simulating-ultrasound-stimulation-in-the-human-brain#post-8677 Tue, 29 Nov 2022 19:22:40 +0000 yichen 8677@http://www.k-wave.org/forum/ <p>Hi Treeby and colleagues,</p> <p>I am trying to simulate ultrasound stimulation in the human brain.<br /> I defined the Kgrid as the size of T1 weighted image, in this case, 192*256*256, with dx=dy=dz=0.8e-3.<br /> I defined the medium using segmentation result which separate skull, soft tissue and scalp, and set each density, sound_speed and alpha_coeff according to literatures.<br /> I set up the source using makeBowl function to mimic a ultrasound transducer.<br /> I set up the sensor so that it covers the whole Kgrid.<br /> I set up the input signal as what 'example_diff_focused_ultrasound_heating' did.</p> <p>The simulation worked well at the first half of computing, while went very strange during the second half, as shown in the figure below.<br /> The following two figures show how the simulation result changes over time. You can access to the figure by the URL.<br /> <a href="https://ibb.co/d60B7ch" rel="nofollow">https://ibb.co/d60B7ch</a><br /> <a href="https://ibb.co/LRFQDS0" rel="nofollow">https://ibb.co/LRFQDS0</a></p> <p>This only happens when I introduced the skull into medium.<br /> Once I removed the skull from the medium, i.e., left the skull part as free water, the simulation became reasonable.<br /> The simulation also works well if I select one X-Y plane and do a 2D simulation, with skull defined in medium.</p> <p>Can you advise what maight account for the strange simulation result above, and how I can modify my code to fix things? I have attached my code for simulation below. Can you also have a look on it? Thanks in advance!</p> <p>P.S.:If you need the segmentation file for replication, please tell me and I'll upload it to somewhere like the google drive.</p> <p>%% Code for simulation<br /> clear; close all; clc;<br /> %% get segmentation<br /> T1_nii = load_nii('final_tissues.nii.gz');<br /> T1_recon = T1_nii.img;<br /> %% specify K-grid<br /> Nx = size(T1_recon,1); Ny = size(T1_recon,2); Nz = size(T1_recon,3); %get T1WI resolution<br /> %x - 1:left to max:right, y - 1:back to max:front, z - 1:bottom to max:top<br /> dx = 0.8e-3; dy = 0.8e-3; dz = 0.8e-3; %get T1WI step<br /> if ~rem(Ny,2)<br /> center_y = Ny/2;<br /> else<br /> center_y = (Ny+1)/2;<br /> end</p> <p>if ~rem(Nz,2)<br /> center_z = Nz/2;<br /> else<br /> center_z = (Nz+1)/2;<br /> end<br /> % create the computational grid<br /> kgrid = kWaveGrid(Nx, dx, Ny, dy, Nz, dz);<br /> %% specify medium, parameter from Fomenko et al., 2020, Elife<br /> medium.density = 1000.*ones(Nx, Ny, Nz);<br /> medium.sound_speed = 1482.*ones(Nx, Ny, Nz);<br /> medium.alpha_coeff = 0.21.*ones(Nx, Ny, Nz);<br /> medium.alpha_power = 1.1;<br /> medium.alpha_mode = 'no_dispersion';<br /> % brain tissues, gm&amp;wm<br /> medium.density(T1_recon==1|T1_recon==2) = 1040;<br /> medium.sound_speed(T1_recon==1|T1_recon==2) = 1552;<br /> medium.alpha_coeff(T1_recon==1|T1_recon==2) = 0.21;<br /> % scalp<br /> medium.density(T1_recon==5) = 1100;<br /> medium.sound_speed(T1_recon==5) = 1732;<br /> medium.alpha_coeff(T1_recon==5) = 0.21;<br /> % bone<br /> % medium.density(T1_recon==7|T1_recon==8) = 1732;<br /> % medium.sound_speed(T1_recon==7|T1_recon==8) = 2850;<br /> % medium.alpha_coeff(T1_recon==7|T1_recon==8) = 2.7;<br /> %% define the transucer<br /> aperture_grid = round(64e-3/dx)+1;<br /> curvature_grid = round(64e-3/dx);<br /> pos_transducer = [1, center_y ,center_z]; %where to put the transducer<br /> source.p_mask = makeBowl([Nx, Ny, Nz], pos_transducer, ...<br /> curvature_grid, aperture_grid, [curvature_grid, center_y, center_z], 'Plot', true);<br /> %% define input signal<br /> % define the acoustic parameters<br /> freq = 5e5; % [Hz] 500KHz<br /> amp = 0.5e6; % [Pa]</p> <p>% calculate the time step using an integer number of points per period<br /> sound_speed = 1482; % [m/s]<br /> ppw = sound_speed / (freq * dx); % points per wavelength<br /> cfl = 0.3; % cfl number<br /> ppp = ceil(ppw / cfl); % points per period<br /> T = 1 / freq; % period [s]<br /> dt = T / ppp; % time step [s]</p> <p>% calculate the number of time steps to reach steady state<br /> t_end = sqrt( kgrid.x_size.^2 + kgrid.y_size.^2 + kgrid.z_size.^2 ) / sound_speed;<br /> Nt = round(t_end / dt);</p> <p>% create the time array<br /> kgrid.setTime(Nt, dt);</p> <p>% define the input signal<br /> source.p = createCWSignals(kgrid.t_array, freq, amp, 0, 0); % ramp_length=0</p> <p>% figure;<br /> % plot(source.p);</p> <p>%% define the sensor mask<br /> % set the sensor mask to cover the entire grid<br /> sensor.mask = ones(Nx, Ny, Nz);<br /> % sensor.record = {'p', 'p_max_all', 'I', 'I_avg'};<br /> sensor.record = {'p', 'p_max_all'};</p> <p>%% run simulation<br /> % record the last 3 cycles in steady state<br /> num_periods = 3;<br /> T_points = round(num_periods * T / kgrid.dt);<br /> sensor.record_start_index = Nt - T_points + 1;</p> <p>% set the input arguements<br /> input_args = {'PMLInside', false, 'PlotPML', false, 'PMLAlpha', 1e6, 'DisplayMask', ...<br /> 'off', 'PlotScale', [-1, 1] * amp, 'Smooth', [false, true, true]};</p> <p>% run the acoustic simulation<br /> sensor_data = kspaceFirstOrder3D(kgrid, medium, source, sensor, input_args{:}); </p> http://www.k-wave.org/forum/topic/alpha-version-of-kwavearray-off-grid-sources/page/2#post-8673 Mon, 28 Nov 2022 15:56:34 +0000 Bradley Treeby 8673@http://www.k-wave.org/forum/ <p>Hi HN,</p> <p>Yes at the moment you need to define them manually. The <a href="http://www.k-wave.org/documentation/example_at_linear_array_transducer.php">Modelling A Linear Array Transducer Example</a> shows one way to do this.</p> <p>Brad. </p> http://www.k-wave.org/forum/topic/alpha-version-of-kwavearray-off-grid-sources/page/2#post-8672 Mon, 28 Nov 2022 13:37:46 +0000 nhaidour 8672@http://www.k-wave.org/forum/ <p>Thank you for your response ! </p> <p>I want to modelise a 2D Probe that contain elements and an inter-space element in 3D, and I think the best way is to use KwaveArray class! But I did not find the function that would allow me to declare the number of elements with an inter-space and their position. Or do I have to declare each element manually? </p> <p>Best Regards,<br /> HN </p> http://www.k-wave.org/forum/topic/alpha-version-of-kwavearray-off-grid-sources/page/2#post-8670 Tue, 22 Nov 2022 21:11:11 +0000 Bradley Treeby 8670@http://www.k-wave.org/forum/ <p>Yes - there are several examples in the included documentation under “modelling transducer arrays”. </p> http://www.k-wave.org/forum/topic/alpha-version-of-kwavearray-off-grid-sources/page/2#post-8669 Tue, 22 Nov 2022 16:12:49 +0000 nhaidour 8669@http://www.k-wave.org/forum/ <p>Hello,</p> <p>Is there some examples for using the KwaveArray ?</p> <p>Best Regards,<br /> HN </p> http://www.k-wave.org/forum/topic/alpha-version-of-kwavearray-off-grid-sources#post-8642 Tue, 08 Nov 2022 10:13:50 +0000 Bradley Treeby 8642@http://www.k-wave.org/forum/ <p>Noting that <code>kWaveArray</code> is now part of k-Wave v1.4. </p> http://www.k-wave.org/forum/topic/alpha-version-of-kwavearray-off-grid-sources#post-8573 Wed, 13 Jul 2022 17:31:30 +0000 bencox 8573@http://www.k-wave.org/forum/ <p>Hi quetaijiangchu and LewisR, </p> <p>There is not such an example yet, no, although the idea behind kWaveArray does have the capability of modelling just such sources. Essentially, given a desired surface, it is necessary to convolve it with the bandlimited interpolant, which has the form <code>sinc(x * pi / dx)</code>, and then sample the resulting function at the grid points to give the weights used in kWaveArray. The details are given in <a href="http://bug.medphys.ucl.ac.uk/papers/2019-Wise-JASA.pdf">this paper</a>. We will add more functionality in due course when we integrate it into k-Wave properly.</p> <p>Best wishes<br /> Ben </p> http://www.k-wave.org/forum/topic/alpha-version-of-kwavearray-off-grid-sources#post-8552 Wed, 15 Jun 2022 08:28:47 +0000 quetaijiangchu 8552@http://www.k-wave.org/forum/ <p>Is there an example of how to create 3D irregularities using function addCustomElement? </p>