Draw on a 3D volume in MATLAB

I have a 3D brain volume (x, y) coordinates and z=slices. For this volume, I have specific coordinates (that reflects some features) and I want to highlight these coordinates (e.g. through drawing with specific color). I searched and found a code like that:

t=image;                 % gray scale image
red=t;
green=t;
blue=t;
for i=1:size(indx,1)     %indx: indexes of the featured coordinates
red(indx(i,1),indx(i,2))=255;
green(indx(i,1),indx(i,2))=0;
blue(indx(i,1),indx(i,2))=0;
end
out=cat(3,red,green,blue);

The problem is that, this code works with gray scale image. When I tried to generalize it to the volume I got something with the size:(x,y,z,3) through:

for i=1:size(indx,1)
red(indx(i,1),indx(i,2),indx(i,3))=255;
green(indx(i,1),indx(i,2),indx(i,3))=0;
blue(indx(i,1),indx(i,2),indx(i,3))=0;
end
out = cat(4, red, green, blue);

Is this generalization right? if so, how to show the resulting slices with the colored parts?

Answer 1

[Walter Roberson]

Yes, that should work, if you use it together with a routine such as vol3d v2 from the File Exchange.

Other viewer routines might prefer that the RGB be the 3rd dimension rather than 4th, but vol3d prefers RGB to be the 4th dimension.

[Fatma Elzahraa Ahmed]

Thank you very much

I tried it in this form

D = squeeze(out);
h = vol3d('cdata',D);

But I get a rendering results without a capability to move through the slices. In addition, the colored areas do not appear in red. I am I miss something?

[Walter Roberson]

I suggest that you have a look in the File Exchange at the various slice routines.

[Fatma Elzahraa Ahmed]

I tried another way. Rather than representing what I need using the color, I draw shapes (e.g plus) to define the needed points. Thank you very much for your help.