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I exported multiple slices of the same series (and the same study) using GDCM in C++. The data is attached here. But it seems that 3D Slicer cannot recognize these files correctly:

  1. Each dcm file was recognized as a volume

enter image description here

  1. After import, nothing is displayed in Slicer.

I think I've filled some inappropriate content into some important dicom Tags. But there are hundreds of tags, how to find which one[s] is[are] inappropriate? How to make these dicom files compatible with Slicer?

What I've tried:

  1. Set the same Study UID and Series UID of each dicom file. [Still the same]
  2. Change to fo-dicom(C#) from GDCM(C++). [Still the same]

Error logs in Python interactor console:

Warning in DICOM plugin Scalar Volume when examining loadable Series Number: Unnamed Series: Reference image in series does not contain geometry information. Please use caution.

Loading with imageIOName: GDCM
Could not read scalar volume using GDCM approach.  Error is: FileFormatError
Loading with imageIOName: DCMTK
Could not read scalar volume using DCMTK approach.  Error is: FileFormatError

Could not load: Series Number: Unnamed Series as a Scalar Volume
Amit Joshi
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Shannon
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  • A quick look at your data shows that you have the meta tag `SourceApplicationEntityTitle` (0002,0016) twice in the dataset, which is illegal. I don't know if this is related to the problem, but you may want to fix this. – MrBean Bremen May 12 '23 at 06:41
  • @MrBeanBremen The duplicated Tag would be ignored by 3D slicer (with a warning in log). I've removed this tag and updated the data. My problem is not resolved. – Shannon May 16 '23 at 01:11

1 Answers1

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According to the information in the Python interactor console, it may caused by a known issue of older Slicer. Can you upgrade 3d Slicer to the latest nightly built version? I can import your DICOM files correctly with version 5.3.0-2023-05-21. As 5.x is better able to handle non-compliant DICOM files.

J. Sue
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  • Great thx! This fixes the immediate problem. – Shannon Jun 03 '23 at 02:21
  • Glade to hear that. But take care of the coodinates & positioning tags. The positon information in your files may be incorrectly. You will find this issue if you goto the Volume Rendering Module. – J. Sue Jun 03 '23 at 02:25