3D Slicer cannot display cardiac LGE MRI volume correctly – only a single line/slice is shown after DICOM import

Support
1

Hello everyone,

I am using 3D Slicer for cardiac MRI (LGE/PSIR) image analysis. My goal is to perform registration and ROI-based analysis between pre- and post-procedure LGE images.

However, I encountered an issue when importing a cardiac PSIR LGE DICOM series.

After loading the DICOM series, 3D Slicer does not display the complete 3D volume correctly.

The problems are:

  • The sagittal view shows part of the cardiac image;
  • The axial/coronal views only show a thin line or a single slice;
  • The 3D view does not display a normal cardiac volume.

It seems that the DICOM series may not have been reconstructed correctly as a 3D volume.

My workflow:

  1. Imported the DICOM folder using the DICOM module;
  2. Selected the PSIR 15 min LGE series;
  3. Loaded the volume into Slicer.

I would like to ask:

  1. Does this problem usually indicate that the DICOM series was not recognized correctly as a 3D volume?
  2. Could this be related to incorrect slice ordering, slice spacing, or missing/incorrect Image Position Patient information?
  3. What is the recommended workflow for importing short-axis cardiac PSIR LGE MRI datasets into 3D Slicer?
  4. Are there any specific DICOM settings or plugins required for cardiac MRI reconstruction?

I attached a screenshot of the issue.

Thank you very much for your help!

402a16c5-efa6-4a3d-9ac0-c8a0f0067249
402a16c5-efa6-4a3d-9ac0-c8a0f00672491760×1288 157 KB

2

You can try enabling advanced mode and selecting on of the other plugins if the default selection is not working.

You can also try the ideas here: https://slicer.readthedocs.io/en/latest/user_guide/modules/dicom.html#troubleshooting

If you are able to share the data probably someone can help you figure it out.