DICOM reconstruction AXIAL to CORONAL & SAGITTAL

How can I do the following with a file filled with 362 dicom AXIAL images of the abdomen.

-Display all slices, and an image of a user-specified slice.

-Extend functionality to display coronal and sagittal views, with user specified location.

I am assuming I should assign each dicom to an array and then display the images that way. I am inexperinced with MATLAB and coding in general. Any help would be appreciated.

Also I cannot use the any Toolbox.

[Rik]

I would suggest you search the file exchange for a dicom viewer. There should be multiple you can use that do not require the image processing toolbox.

[Mahmoud Ghanim]

I am not allowed to use DICOM viewer. This needs to be coded.

[Walter Roberson]

My estimate of the time required to complete that project is approximately 3 years, if you are very skilled.

The DICOM standard is huge. The work of displaying those images and everything else you list there is trivial compared to the work you will have to put in to build a DICOM reader from scratch.

(The DICOM reader function is part of the Image Processing Toolbox, but you are not permitted to use any toolboxes.)

[Rik]

Well, you could use this FEX entry by Dirk-Jan Kroon to read the dicom info. That is a great start. After that you can use the pixel data field for most of the imaging formats.

What exactly are you required to code yourself? And why? It is all about standing on the shoulders of giants. And how is code provided here by us any different from code on the FEX?

[Walter Roberson]

Using a FEX contribution would be equivalent to using a toolbox, I am sure.

[Mahmoud Ghanim]

I have 22 axial DICOM (.dcm) images. I 1st use this formula to assign them to volume V.

>[V,s,d] = dicomreadVolume(fullfile('CT'));

I divide V by 288 to see the images.

>a = V*288;

Then I use implay to view the axial images as a movie.

>implay (b,1);

Axial images are the view from z axis. I need to do the same thing in the x-axis and in the y-axis.

I am supposed to add a user input function to display the frame based off of the prefrence of the user. So promet the user with "What slice would you like to see", they enter 5, the video would start at the 5th frame.

I am then required to generate a 2D projection image from a the 3D volumetric image using the parellel beam geometry by summing the voxel intensity along each slice.

[Rik]

The dicomreadVolume function is part of the Image Processing Toolbox, so already on your first line of code you're violating one of your rules.

Your second line doesn't make sense, since you are not dividing V, but multiplying it. That line also doesn't do anything to make you see the images, nor are you using the result next.

The third line of code is confusing as well, as b was not previously defined. (and implay is in the IPT as well)

So what is your question? If you're allowed to use toolboxes after all, what is the reason you can't adapt an existing viewer from the FEX to suit your particular requirements?

[Mahmoud Ghanim]

I made adjustment before replying to the thread , copied then pasted the wrong information. Code runs like this:

>[V,s,d] = dicomreadVolume(fullfile('CT'));

>a = V*288;

>implay (a,1);

CT is were the images sit. I guess the professor wants us coding using whats defaulted on MATLAB. There is a DICOM Viewer, Rik, that has everything I need, but its not how I was instructed to do it.

This is more of a math problem then a coding problem. Think of axials coronals and sagitals as i j k in a matrix. I am just not savy enough to figure it out.

I need to basically transform the matrix. I think....

[Rik]

It is not clear to me what your problem is, but it now sounds like you should be looking at the permute function to easily exchange dimensions.

Maybe it would help to share the exact assignment and point us to the parts where you have trouble finding a solution.

[Mahmoud Ghanim]

1. Write a Matlab program to open all slices from the “CT_Abdomen” image set and display the image of a user-specified slice.

2. Extend the functionality so that it can display the axial, coronal and sagittal view of a userspecified location?

3. Generate a 2D projection image from the 3D volumetric image using the parallel beam geometry by summing the voxel intensity along each beam.

The slices are 280 dicom (.dcm) images.

[Walter Roberson]

One thing I worry about is the possibility that the data might be integer class, so multiplying by 288 might lead to overflow.

"288" looks dangerously magic. Why 288?

Extracting perpendicular views is just a matter of indexing, possibly with a squeeze() or permute() thrown in.

See also radon()

[Rik]

I guess boldly:

If the multiplication by 288 is intended to make your CT use more of the display range in terms of greyscale, you shouldn't do that by modifying the data. Instead you should modify the caxis. You can either write something yourself, or you can implement my WindowLevel FEX submission. (Also, in that assingment you posted I see nothing about not being allowed to use code from a toolbox or the FEX.)