Error in exporting .tiff images to DICOM

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1

Hello,

I have .tiff files of a lung phantom that I want to export to DICOM files using 3D Slicer (4.11.20200930 or 4.13.0). I was able to import the .tiff files into 3D Slicer and export them to DICOM. But when I tried to import the files from the DICOM database into the scene, the scene turns out all black. I do not understand why.

Thank you for your help.

2

Are there any warnings or errors in the application log?
Can you upload the exported data set somewhere and post the link here so that we can have a look?

3

Hi Andras,

Thank you for your prompt reply.
No, there is a message saying ‘create a DICOM Series completed without errors’.

Here is the link for the .tiff files:

And for the exported DICOM data:

I am sorry for not making the link public. They are part of a research project. So, I just shared the link with your email.

4

The problem is that values in these TIFF files are stored very poorly:

  • it has floating-point values, while voxels have 15-20 discrete values, which makes it hard to assign any meaning to voxel values
  • range of values is between -0.0048 and 0.0531 (until very recently DICOM only supported storage of integer values, and for compatibility reasons we still use only integers; since all input voxels are approximately 0, all voxels in the exported DICOM volume are set to 0, too)

You can fix everything by using Simple Filters module -> RescaleIntensityImageFilter or ShiftScaleImageFilter. CT volumes typically scaled between -1000 and 1000. If you set this output range then everything will work well

I would recommend to notify the group that created the volumes to switch to using standard 3D volume file formats, such as NRRD, instead of multi-frame 2D TIFF image.

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