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k-Wave User Forum » User Favorites: yichen yichen Support for the k-Wave MATLAB toolbox en-US Tue, 12 May 2026 23:39:12 +0000 http://bbpress.org/?v=1.0.2 <![CDATA[Search]]> q http://www.k-wave.org/forum/search.php quetaijiangchu on "Simulating ultrasound stimulation in the human brain" 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/ Can share this file if allowed('final_tissues.nii.gz')？ sky on "Simulating ultrasound stimulation in the human brain" 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/ You can give me that file ('final_tissues.nii.gz'), and how do you run load_nii yichen on "Simulating ultrasound stimulation in the human brain" 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/ Thank you Treeby! Your advice helps a lot! Bradley Treeby on "Simulating ultrasound stimulation in the human brain" 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/ Broadly speaking, that sounds right. See <a href="//www.k-wave.org/documentation/makeBowl.php”">the docs</a>. yichen on "Simulating ultrasound stimulation in the human brain" 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/ Thank you Treeby. I think it's the issue of CFL setting resulting in instability. After I reduced the CFL from 0.3 to 0.2, the simulation became reasonable. 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? %% define the transducer radius = round(64e-3/dx); %transducer curvature in grid step diameter = round(64e-3/dx)+1; %transducer diameter in grid step pos_transducer = [96, 170 ,211]; %where to put the transducer focus_transducer = [96, 148, 167]; %where the ultrasound to be focused source.p_mask = makeBowl([Nx, Ny, Nz], pos_transducer, ... radius, diameter, focus_transducer, 'Plot', false); 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. As to the 'pos_transducer', it refers to the coordinate of the center of the transducer. As to the 'focus_transducer', it refers to the coordinate of the brain region we are intended to stimulate. Thanks again for your assistance! yichen on "Simulating ultrasound stimulation in the human brain" 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/ Thanks for your reply. I'll try with reducing CFL and get back to you later. Bradley Treeby on "Simulating ultrasound stimulation in the human brain" 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/ I haven't run your simulation, but it looks a lot like classic instability. Does it work if you reduce the CFL? yichen on "Simulating ultrasound stimulation in the human brain" 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/ Hi Treeby and colleagues, I am trying to simulate ultrasound stimulation in the human brain. I defined the Kgrid as the size of T1 weighted image, in this case, 192*256*256, with dx=dy=dz=0.8e-3. 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. I set up the source using makeBowl function to mimic a ultrasound transducer. I set up the sensor so that it covers the whole Kgrid. I set up the input signal as what 'example_diff_focused_ultrasound_heating' did. The simulation worked well at the first half of computing, while went very strange during the second half, as shown in the figure below. The following two figures show how the simulation result changes over time. You can access to the figure by the URL. <a href="https://ibb.co/d60B7ch" rel="nofollow">https://ibb.co/d60B7ch</a> <a href="https://ibb.co/LRFQDS0" rel="nofollow">https://ibb.co/LRFQDS0</a> This only happens when I introduced the skull into medium. Once I removed the skull from the medium, i.e., left the skull part as free water, the simulation became reasonable. The simulation also works well if I select one X-Y plane and do a 2D simulation, with skull defined in medium. 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.S.:If you need the segmentation file for replication, please tell me and I'll upload it to somewhere like the google drive. %% Code for simulation clear; close all; clc; %% get segmentation T1_nii = load_nii('final_tissues.nii.gz'); T1_recon = T1_nii.img; %% specify K-grid Nx = size(T1_recon,1); Ny = size(T1_recon,2); Nz = size(T1_recon,3); %get T1WI resolution %x - 1:left to max:right, y - 1:back to max:front, z - 1:bottom to max:top dx = 0.8e-3; dy = 0.8e-3; dz = 0.8e-3; %get T1WI step if ~rem(Ny,2) center_y = Ny/2; else center_y = (Ny+1)/2; end if ~rem(Nz,2) center_z = Nz/2; else center_z = (Nz+1)/2; end % create the computational grid kgrid = kWaveGrid(Nx, dx, Ny, dy, Nz, dz); %% specify medium, parameter from Fomenko et al., 2020, Elife medium.density = 1000.*ones(Nx, Ny, Nz); medium.sound_speed = 1482.*ones(Nx, Ny, Nz); medium.alpha_coeff = 0.21.*ones(Nx, Ny, Nz); medium.alpha_power = 1.1; medium.alpha_mode = 'no_dispersion'; % brain tissues, gm&wm medium.density(T1_recon==1|T1_recon==2) = 1040; medium.sound_speed(T1_recon==1|T1_recon==2) = 1552; medium.alpha_coeff(T1_recon==1|T1_recon==2) = 0.21; % scalp medium.density(T1_recon==5) = 1100; medium.sound_speed(T1_recon==5) = 1732; medium.alpha_coeff(T1_recon==5) = 0.21; % bone % medium.density(T1_recon==7|T1_recon==8) = 1732; % medium.sound_speed(T1_recon==7|T1_recon==8) = 2850; % medium.alpha_coeff(T1_recon==7|T1_recon==8) = 2.7; %% define the transucer aperture_grid = round(64e-3/dx)+1; curvature_grid = round(64e-3/dx); pos_transducer = [1, center_y ,center_z]; %where to put the transducer source.p_mask = makeBowl([Nx, Ny, Nz], pos_transducer, ... curvature_grid, aperture_grid, [curvature_grid, center_y, center_z], 'Plot', true); %% define input signal % define the acoustic parameters freq = 5e5; % [Hz] 500KHz amp = 0.5e6; % [Pa] % calculate the time step using an integer number of points per period sound_speed = 1482; % [m/s] ppw = sound_speed / (freq * dx); % points per wavelength cfl = 0.3; % cfl number ppp = ceil(ppw / cfl); % points per period T = 1 / freq; % period [s] dt = T / ppp; % time step [s] % calculate the number of time steps to reach steady state t_end = sqrt( kgrid.x_size.^2 + kgrid.y_size.^2 + kgrid.z_size.^2 ) / sound_speed; Nt = round(t_end / dt); % create the time array kgrid.setTime(Nt, dt); % define the input signal source.p = createCWSignals(kgrid.t_array, freq, amp, 0, 0); % ramp_length=0 % figure; % plot(source.p); %% define the sensor mask % set the sensor mask to cover the entire grid sensor.mask = ones(Nx, Ny, Nz); % sensor.record = {'p', 'p_max_all', 'I', 'I_avg'}; sensor.record = {'p', 'p_max_all'}; %% run simulation % record the last 3 cycles in steady state num_periods = 3; T_points = round(num_periods * T / kgrid.dt); sensor.record_start_index = Nt - T_points + 1; % set the input arguements input_args = {'PMLInside', false, 'PlotPML', false, 'PMLAlpha', 1e6, 'DisplayMask', ... 'off', 'PlotScale', [-1, 1] * amp, 'Smooth', [false, true, true]}; % run the acoustic simulation sensor_data = kspaceFirstOrder3D(kgrid, medium, source, sensor, input_args{:});