Display 3D volumes with different colours in the surface

Dear all,

I'm working with brain MRI images and as a result I obtain statistical maps (values between 0 and 25) which I would like to represent in 3D with a colormap. I have x, y and z coordinates, and stat(the statistical value which I want to represent in color). I used a nice function called PATCH_3Darray, calling patch for each voxel, and I obtained this image:

I would like to smooth the voxels, so they do not seem bricks and don't have corner-edges. How could I smooth all if there are individual patches?

I was considering binarizing my statistical image, get connected voxels, create an isosurface like: BW=statistical_image>0; CC = bwconncomp(BW); L = labelmatrix(CC); color=hsv(15);

for i=1:1:numel(unique(L)) A=(L==i); e = patch(isosurface(A,0.5), ... 'FaceColor', color(i,:), 'EdgeColor', 'none'); hold on end

and somehow get in the surface/"face" of each object the real values in the matrix statistical_image (as in the first image), colored with a colormap. How could I do it? Please, could you help me with code?

Thank you very much, All the best,

Úrsula

Answer 1

[UrsulaPR]

Hi,

I solved the problem using isosurface and a nice function,"smooth triangulated mesh" https://es.mathworks.com/matlabcentral/fileexchange/26710-smooth-triangulated-mesh:

% dims: image dimensions

axx=1:dims(1); ayy=1:dims(2); azz=1:dims(3); [xgrid,ygrid,zgrid] = meshgrid(axx, ayy, azz);

%statistical_image

%binary_statistical_image: assuming only positive values, put 1s where %statistical_image > 0

[faces,verts,colors] = isosurface(xgrid,ygrid,zgrid,binary_statistical_image,0.99999,statistical_image,'','verbose');

addpath('smoothpatch_version1b') mex smoothpatch_version1b\smoothpatch_curvature_double.c -v

mex smoothpatch_version1b\smoothpatch_inversedistance_double.c -v

mex smoothpatch_version1b\vertex_neighbours_double.c -v

FV.vertices=verts; FV.faces=faces; FV_smoothed=smoothpatch(FV,1,5); hpatch=patch(FV_smoothed, ... 'FaceVertexCData', colors, ... 'FaceColor','interp', ... 'edgecolor', 'interp');

Hope this helps,

All the best, Úrsula

Answer 2

[KSSV]

Try/type shading interp after plotting the figure.

Answer 3

[UrsulaPR]

Thank you KSSV,

I already tried shading interp but I get "Warning: Color Data is not set for Interpolated shading# multiple times.

The input to patch3D_array is a matrix with NaN in nonsignificant voxels, and the statistical value in the significant voxels. The call is [hpat,hcbar] = PATCH_3Darray(statistical_map,cmap,'col').

Inside patch3D_array (downloaded from Matlab Central), there is a handle for each patch hpat{loopJ} = patch(xco,yco,zco,cmap(loopJ,:));

Would you suggest a different way to represent my data, instead of PATCH3D_array?

Thank you very much,

Úrsula

Answer 4

[UrsulaPR]

Dear all,

I tried with isocolors and even though I didn't get what I expected, hopefully I'm improving. The code I tried is:

% 'activation' is the statistical volume, with values between 0 and 30. % 'dims' are the dimensions of the image. % Get a binary version, for isosurface:

activation_binary=zeros(size(activation)); activation_binary(activation>0)=1;

% Isosurface of all the activation clusters

[x,y,z] = meshgrid(1:dims(1),1:dims(2),1:dims(3)); p = patch(isosurface(smooth3(activation,'gaussian',[3 3 3]'),0.5));

% Isonormals and isocolors, trying to put the "activation" statistical values as a color

isonormals(x,y,z,activation,p) isocolors(x,y,z,activation,p) set(p, 'FaceColor', 'interp'); set(p, 'EdgeColor', 'none'); alpha(p,1)

% Custom color map yellow-orange-red

RGB_yellow=[255,255,0]; RGB_orange=[255,123,0]; RGB_red=[255,0,0]; T=vertcat(RGB_yellow,RGB_orange,RGB_red)./255; % %T = [255,255,0;255,123,0;255,0,0]./255; max_number=numel(unique(activation)); x = [0, max_number/2, max_number]; cmap = interp1(x/max_number,T,linspace(0,1,max_number));

% Color the surface

colormap(cmap);colorbar axis vis3d tight

The figure is:

I visualize a volume with different colors in the surface, but not the correct colors, they should be from a bit above 0 to 30. Please, do you have any suggestions?

Thank you very much and sorry for the long email.

All the best,

Ursula