Dicom directory (of slices) to 3D volume image

Read a series of dicom slice images to a 3D volume image and meta data.

Description

This function reads all good dicom files in a given directory and outputs a volume image. The slices are sorted by the SliceLocation tag in the image header. If no directory is specified, it opens a folder browser.

It also collects user specified (or default) header information for each slice and calculates some additional data for each slice such as the physical width and height of the image (e.g. PhysicalWidth = PixelWidth(1)*Rows). It also determines some meta data about the image such as the physical aspect ratio which is useful for volume rendering utilities.

Finally, it saves all the data to the dicom directory as a MAT file. In the future, the user will be able to switch the file saving on and off, and also specify alternate formats.

Acknowledgements

The author wishes to acknowledge the following in the creation of this submission:
3D Free Form Image Registration Toolbox (GUI), Read and write single file dicom volumes, isdicom

• MATLAB release: MATLAB 7.7 (R2008b)
• Other requirements: isdicom http://www.mathworks.com/matlabcentral/fileexchange/11431

[WILLIAM]

Hey, I'm really excited about the prospect of having a DICOM file viewer in MATLAB. Unfortunately, I get the following error when running dicom23D:

?? Index exceeds matrix dimensions.

Error in ==> dicom23D at 218
    if isfield(slice_data(1), 'SliceLocation')

[Ariel Balter]

I think it is possible that you tried it on an empty directory -- at least that is how I could reproduce the error you got.

In any case, I just uploaded an updated version with improvements and more catches. Please let me know how it works for you. --AB

[Tangarua Tangarua]

Hi Unfortunately, I am getting a similar error:
ans =

header did not contain the field SpacingBetweenSlices

??? Index exceeds matrix dimensions.

Error in ==> dicom23D at 270
    [rows, cols] = size(slice_data(1).SliceData);

Could you please help me to figure that out?
If you need my DICOM files, just send me an email and I'll send them to you.

Best Regards

[Hakan Gustafsson]

Hi,
I also have the same problem :-( DICOM from a Philips achieva.

Best regards,
Håkan

[Crtistian Capannini]

THIS MUST BE FIXED!!

[Ariel Balter]

Sorry, I made that for a project I have long since abandoned. I don't use dicom or do any imaging stuff any more at all.

Nevertheless, I will try to take a look and see if I can fix it. At the very least I will extensively comment in the hopes that someone else can debug.

Again, sorry for it not working out of the box.

[helena]

 

[Haseeb]

Hi,
I was able to get a mat file running the dicom23D function. How do I use this output? Can I visualize the data?
Thanks,
Haseeb

[Mitchell Blenden]

Will this code allow me to take Philips 3D data from their 3D echo and play it in matlab? Also will this allow me to make a 3D image from their data. The rep says the file is 3D dicom native data and I can not find out how to load it in as a 3D image, it only comes into matlab as a 2D image.
Thanks!

[Mitchell Blenden]

 

[Ariel Balter]

Folks, I'm sorry, but I can't support this script at this time. I'm inclined to pull it, but since some folks are getting some use out of it, I'll leave it up for the time being.

The code is pretty well commented, so I think it should be possible for someone to get it working, and I'd be happy to update with bug fixes as they come in.

I wrote this code a long time ago when I was doing a specific project with dicom files. That was the last time I looked at such files, and I no longer have any to test with.

Good luck!

[bahar cham]