Export DICOM in Colors

Dear all,
I imported a set of DICOM files to Slicer. These DICOMs are for 3D echo doppler so they are colorful. Then, I export them in “Data” → “Export to DICOM” in the right-click menu. The exported files are grayscale. I tried to change the rendering in “Volume”, but can not fix the problem. Any insights?

thanks,
Alan

There is no widely used standard for 3D ultrasound (usually the 3D voxel data is stored as private fields in DICOM) and Doppler is even more hopeless.

What is the complete workflow that you are trying to implement? Where does the Doppler data comes from, what would you like to do with it in Slicer, and what software you want to process the exported data with?

Is your 3D echo Doppler data set is 2D+time (you have a time sequence of a colored slice) or 3D+time (you have a 3D array of voxels, each voxel having a 3D vector value)?

Thanks for your reply.

I do not need to process the image. The only steps I need to do are:

  1. Click “Add Data” à “Choose Directory to Add” and select a directory that contains a set of DICOM files to Slicer. This set of DICOM files, similar to MRI images, represent slices of anatomy at one time point.
  2. Modules → “Data” → “Export to DICOM” in the right-click menu.

The problem is that the exported files are grayscale, while I wish they were colorful (the original data was in color).

Thanks,

Alan

Do you get a Cartesian color Doppler 3D volume from DICOM? Do each voxel contain a speed vector, or just an RGB image that contains the B-mode image fused with some color overlay?

What software generates these volumes?

How do you visualize these images in Slicer? Can you attach a screenshot?

We haven’t implemented color image DICOM export (these color images are usually just screenshots that do not have much use other than visualization), but if your input images are already color DICOM images and you don’t process them in Slicer, then you may not need to re-export them.

Blockquote
We haven’t implemented color image DICOM export (these color images are usually just screenshots that do not have much use other than visualization), but if your input images are already color DICOM images and you don’t process them in Slicer, then you may not need to re-export them.

I do not process my DICOM set in Slicer but need to process them in another software. However, somehow, that software does not recognize my DICOM set as one sequence, meaning if I load them, the software only read them seperately not one sequence of images as a whole. I need to do this “Import” and " Export" in Slicer then the software will recognize the exported DICOMs as a sequence. Unfortunately, the “Export” DICOM is grayscale. Any workaround you can think of to get the DICOM back to colored ones?

Thanks,
Alan

You can edit patient ID (maybe also name, birth date, etc) and study instance UID fields in the exported DICOM data set using dcmodify.exe (command-line tool in DCMTK) or pydicom.

However, this will not change the fact that most software will not allow you to use color images for any kind of analysis or quantification. This is why color image is not useful in general and export was not implemented in Slicer (we need to prioritize to work on features that are clinically useful).

Probably what you need is to export segmentation as DICOM Segmentation Object or DICOM RT structure set. Treatment planning or surgical planning software can then display those as color overlays on the images and also use for planning and analysis.

Sounds great. Thanks for your prompt response!

Alan