How can I build a 3D volume from Dicom files ?

This question has indeed been asked several time, but i never managed to find an appropriate answer to my case.

I have 3 types of images :

SLX+0.dcm, SLX+1.dcm, SLX+2.dcm...
SLX-1.dcm, SLX-2.dcm, SLX-3.dcm... %without number 0

%%and the same scheme with SLY and SLZ.

I thought first i would need to pile them or even imbricate them into an array but it seems irrelevant to me since it has "3" plans...

What logic should I use in that case to rebuild the volume ?

thank you

Answer 1

[Sean de Wolski]

My answer here may interest you:

http://www.mathworks.com/matlabcentral/answers/43386#answer_53269

If it doesn't answer your question, please be specific about what you have and what you need.

Answer 2

[ocelote]

Thank you for your prompt answer. I actually would like to build a 3D volume from my DICOM file. My issue here is to understand how in practice it should be done : how to create a relevant array which will represent my volume.

I will try to explain myself :

I have slices in the direction X, Y and Z (my dicom files). Slices are separated each other by a tiny distance when they are in the same direction (data acquisition)

But this doest fit with the structure of an array [X, Y, Z] because i can only stack one direction and build a 3D array of X plan, another 3D array for Y and another for Z whilst i wish to be able to visualize this 3D dicom.

it seems i need to mix "three" 3D array in one :x but i must have forgotten smth since other ppl managed to see 3D dicom object...

Answer 3

[ocelote]

I just made a better image to explain/show my issue.

Orange = X axis green = Y axis Purple = Z axis

The spaces between each layer represent the spaces made by the data aquisition. every block represents a voxel.

When i superpose X, Y and Z there are still holes inside my volume (scroll a bit on the right to see)...

So even if i manage to set up a loop which fill an array this way, i ll still not have a complete volume :/

Am I going wrong to rebuild a 3D volume ?

[Sean de Wolski]

Well if you don't have data available at these spots, you could interp3 or griddedInterpolant to fill in the voids or to produce a uniform stride of your data.

[ocelote]

So you suggest me to work pixel by pixel (is there a function at least ?) ? It wont be too much to process smth like 500*500 pixel of my .dcm file? :/

im a matlab beginner and feel completely lost, sry for asking that much.

thank you by the way.

[Sean de Wolski]

You're welcome!

I am suggesting that your interpolate to an even grid, at least in two dimensions, so that you can work on this array like any other 3d array.