Regarding simulated intensity

Orr Zohar — Mon, 24 Feb 2020 18:20:03 -0000

Hello all,
I was wondering what are the units of the simulated intensity.

For example, in TOAST++ Tutorial 1&2, we essentially simulated the measured intensity from different detectors. what are you units for said detectors?

I am asking this as i am trying to understand weither I can gain any insite into the actual detectability of the simulation.

Best regards,
Orr

Way to perform bioluminescence tomography

Emmanuel Cosnard — Fri, 03 May 2019 13:35:24 -0000

Hello,

I am trying to use toast++ to perform fluorescence and bioluminescence tomography.
It is well explained how to perform fluorescence tomography and I am really amaised to have the possibility to use such a great tool simplifying my reseach!

I am now strugling to perform bioluminescence tomography.
Am I right to think that we can perform bioluminescence tomography with toast++ by using the toastReconMultispectralCW function and setting the light source term "qvec" as a zero vector ?

Thank you for your help and regards,

Emmanuel

Inverse model in FDOT_recon_CW_Proj

Emmanuel Cosnard — Fri, 03 May 2019 13:31:41 -0000

Hello,

I am trying to run the example to perform 3D forward and inverse modelling in DOT with FDOT_recon_CW_Proj.m (under examples\matlab\fluorescence).
The forward model seems to work perfectly, and I am actually really glad and grateful to be able to use such a great tool!

Non the less, the inverse model here doesn't seem to work fine, as the system doesn't encounter the concentrations, and the vector describing the concentration, 'x', is filled with only NaN (not a number).

I didn't change anything and used the function as it is given on gitHub.

Has anyone already seen this problem and knows how to solve it?

Thank you,

Emmanuel

error in toastmesh command

sristi das — Thu, 11 Apr 2019 14:07:00 -0000

I am trying to build a spherical mesh in toast++ but I am facing some problem while importing the mesh from gmsh to matlab. On running the following command from matlab prompt:
mesh = toastMesh('sphere.msh','gmsh')
I get the following error:

Attempt to reference field of non-structure array.

Error in toastReadGmshMesh (line 11)
vtx = gmsh.POS;

Error in toastMesh (line 78)
obj = toastReadGmshMesh(arg1);
Can you please tell me why am I getting this error?

3D solver tutorials for Matlab?

Shiqi Xu — Mon, 11 Dec 2017 18:57:54 -0000

Just wondering if there are any 3D foward/inverse tutorials for Matlab user that teach how to create 3D mesh mapped with customed mua/mus, source/detectors and generate frequency domain data. Thanks.

Some questions about mesh in Toast

Dustin Qi — Thu, 25 May 2017 07:20:43 -0000

Now I'm modelling the complete problem of photoacoustic tomography, which means that I need to use TOAST to simulate the light propagation, and then use k-wave toolbox(another matlab toolbox) to model sound propagation. That is, the output from TOAST should be the input of k-wave toolbox. 
But k-Wave and TOAST use different numerical techniques (regular mesh in k-Wave and irregular mesh in TOAST), I don't know how to solve the problem. One way maybe interpolate the function from the nodes of the TOAST basis onto the points in the k-Wave basis in Matlab. But I don't know how to achieve it and  whether it's reliable and accurate. Is there anybody here and help me? Are there some information, papers or examples about it? Any answer would be helpful.
  Thanks.

There is a problem with first reconstruction model(GUI)

Chang, Tai-Jui — Wed, 10 May 2017 05:47:38 -0000

I would like to know how to put the testing data in to the GUI.
Because I fail many times.
This is the first reconstruction test.
To run a simple test reconstruction,I just follow these steps on your websites
Here is the matlab error message that describing the problem I met.
(My computer is x64, Windows10. Matlab:R2016b)

recon_gui
Warning: parameter file not in current working directory.
Changing directory to C:\Users\Louis Chang\Desktop\Toastdic\toast\test\2D\matlab\

Starting reconstruction

Error using toastRecon>checkprm (line 199)
Required parameter field "solver.basis" is missing.

Error in toastRecon (line 28)
[prm LPRM] = checkprm(prm);

Error in recon_gui>runrecon_Callback (line 219)
toastRecon(prm);

Error in gui_mainfcn (line 95)
feval(varargin{:});

Error in recon_gui (line 42)
gui_mainfcn(gui_State, varargin{:});
Error while evaluating UIControl Callback

I would like to know how can I solve this.
I have seen the other discussion about this. But that did not help at all.
Thanks!!
Chang, Tai-Jui

The use of high-order basis functions in the forward solver

Martin Schweiger — Mon, 01 Aug 2016 12:44:41 -0000

Ok, first we should try to figure out the "node without pixel support" problem. This would be caused by the specified bounding box being smaller than the mesh extents. This might be caused by rounding errors. You could just try to create the basis mapper without explicitly specifying a bounding box. Toast then automatically calculates the bounding box from the mesh extents, I.e.

basis = toastBasis(mesh,grd);

The second problem of ending up with inf values in the system matrix may be a result of the first problem.

Can you let me know if this solves the problem? Otherwise I'll look into this in more detail.

The use of high-order basis functions in the forward solver

Dmytro Shulga — Mon, 11 Jul 2016 14:43:16 -0000

Hello Toast++ team,

I would like to use high-order basis functions in the forward solver. Unfortunately, I have some troubles with that. My code with explanations is provided below:

1) I am using Matlab 2016a PDE Toolbox to generate mesh:

g = [    4.0000    4.0000    4.0000    4.0000
  -25.0000    0.0000   25.0000    0.0000
    0.0000   25.0000    0.0000  -25.0000
   -0.0000  -25.0000         0   25.0000
  -25.0000         0   25.0000   -0.0000
    1.0000    1.0000    1.0000    1.0000
         0         0         0         0
         0         0         0         0
         0         0         0         0
   25.0000   25.0000   25.0000   25.0000
   25.0000   25.0000   25.0000   25.0000
         0         0         0         0];
model = createpde(1);
pg = geometryFromEdges(model,g);
msh = generateMesh(model,'Hmax',6,'GeometricOrder','quadratic');
figure; pdeplot(model);

2) The generated mesh is passed into Toast++ “toastMesh” function along with quadratic basis functions type:

vtx = msh.Nodes';
idx = msh.Elements';
eltp = ones(size(idx,1),1)*6;
mesh = toastMesh(vtx,idx,eltp);
figure; mesh.Display;

3) I set up the scattering and absorption coefficients as follows:

mua0 = 0.01;
mus0 = 1.0;
Musfun0 = [num2str(mus0) '*cos(0.15.*x).*cos(0.15.*y)/2 + ' num2str(mus0)];
Muafun0 = [num2str(mua0) '*sin(0.15.*x).*sin(0.15.*y)/2 + ' num2str(mua0)];
Mua0 = ['@(x,y)' Muafun0];
Mus0 = ['@(x,y)' Musfun0];
MuaFunc = str2func(Mua0);
MusFunc = str2func(Mus0);
ref_bkg = 1.0;
nnd = mesh.NodeCount;
ref = ones(nnd,1) * ref_bkg;
N = 1024;
[gx1,gx2] = ndgrid(linspace(-25,25,N),linspace(-25,25,N));
MUA= MuaFunc(gx1,gx2);
MUS = MusFunc(gx1,gx2);
grd = size(MUA);
bb = [-25 25
      -25 25];

4) I call “toastBasis” function:
basis = toastBasis(mesh,grd,grd,bb,'LINEAR');

and get warnings: “Node without pixel support found”. What does this message mean? What is wrong?

5) Finally, I set up sources and detectors

nq = 16;
rad = 25;  %mesh radius [mm]
for i=1:nq
  phi_q = 2*pi*(i-1)/nq;
  Q(i,:) = rad * [cos(phi_q) sin(phi_q)];
  Q(i,:) = [24 0];
  phi_m = 2*pi*(i-0.5)/nq;
  M(i,:) = rad * [cos(phi_m) sin(phi_m)];
end
mesh.SetQM(Q,M);
hold on
plot(Q(:,1),Q(:,2),'ro','MarkerFaceColor','r');
plot(M(:,1),M(:,2),'bs','MarkerFaceColor','b');

% Create the source and boundary projection vectors
qvec = mesh.Qvec('Isotropic', 'Gaussian', 4);
mvec = mesh.Mvec('Gaussian', 2);

% Solve the FEM linear system
K = dotSysmat (mesh,mua,mus,ref,0);

and end up with a system matrix K which contains “inf” and “-inf” values.

What is wrong with my code? Could you help me to understand how to use high-order basis functions in Toast++?

This is an info about my setup:
Mac OS X Yosemite 10.10.5
Matlab R2016a
Toast++ 2.0.0 with precompiled binaries downloaded from https://sourceforge.net/projects/toastpp/files/

Thank you very much for your help.

Some problems regarding mvec, negative values, and non-diffusive regions

Martin Schweiger — Fri, 13 May 2016 15:18:10 -0000

To 1: The relationship between surface exitance \Gamma and volume photon density \phi is given by the Robin b.c.:

\Gamma = -c \kappa \nabla_n \phi
\phi + 2 \kappa A \nabla_n = 0

==> \Gamma = c/(2A) \phi

where \kappa is the diffusion coefficient, A is a parameter that takes into account the effects of the refractive index mismatch at the tissue-air interface, and \nabla_n is the gradient in outward normal direction.

The measurement projection vector, mvec, projects \phi to the surface exitance \Gamma, and integrates \Gamma over the detector profile.

M_i = \int_surface \Gamma(s) \sigma_i(s) ds

where \sigma_i(s) is the measurement sensitivity profile of the i-th detector on the surface.
Therefore, mvec(i,j) = c/2A sigma_i(r_j)
where r_j is the position of the j-th node (nonzero only for boundary nodes).

The "TrigBasis" profile is experimental and can safely be ignored for now. It builds a distributed source or measurement pattern from a cosine basis. Currently it works only for circular 2D problems, and hasn't been tested well.

To 2: Negative values for Phi usually indicate an insufficiently resolved mesh. Try different mesh resolution and check the behaviour. Often, a higher local node density may be needed close to sources, detectors and high-contrast inclusions.

More rarely, it could indicate a node order problem in the mesh. You can check that with mesh.ElementSize. All values should be positive.

To 3: Non-diffuse regions are currently not supported in the Toast++ toolbox. We did some experiments with different approaches (hybrid diffusion/radiosity approach, P_N approximation, but they are not yet part of the toolbox.

Recent posts to Discussion

Regarding simulated intensity

Way to perform bioluminescence tomography

Inverse model in FDOT_recon_CW_Proj

error in toastmesh command

3D solver tutorials for Matlab?

Some questions about mesh in Toast

There is a problem with first reconstruction model(GUI)

Starting reconstruction

The use of high-order basis functions in the forward solver

The use of high-order basis functions in the forward solver

Some problems regarding mvec, negative values, and non-diffusive regions