slice spacing in fluoroscopic angiography

Support
1

Operating system: Ubuntu 22.04.2 LTS
Slicer version:5.2.2
Expected behavior: There is an image spacing warning on DICOM load of a fluoroscopic angiogram. Expect an edit of image spacing in the Volumes module to be sustained at least for the session.
Actual behavior: After one or two clicks on the image panes the image spacing reverts to the wrong initial one. How to make an image spacing correction be retained?

2

Slicer loads fluoroscopy images are time sequences: each timepoint is a separate image. You can apply a transform to change the physical scale of the entire sequence at once.

You could change the spacing of all images in the series by a few Python commands. However, what we see is that if someone uses Slicer (and not a basic 2D viewer) then fluoro images end up fused with 3D images, and then changing the pixel spacing is insufficient, but you need to compute a full projection transform.

What do you do with fluoro images in Slicer? Do you do just basic 2D visualization and measurements or you fuse them with 3D?

3

Thank you — this gives me good reason to learn the Slicer-python interface. Any pointers on the precise python lines to apply the code? I wish to perform image by image segmentation and measurement then aggregate the frame-wise result into 2DxT ~ 3D-ish.

4

Something like this should work:

volumeSequenceNode = slicer.mrmlScene.GetFirstNodeByClass("vtkMRMLSequenceNode")

# Modify spacing in all nodes in the sequence
for volumeIndex in range(volumeSequenceNode.GetNumberOfDataNodes()):
    volumeNode = volumeSequenceNode.GetNthDataNode(volumeIndex)
    volumeNode.SetSpacing(2.0, 2.5, 1.4)

# Force update of volume node from sequence
sequenceLogic = slicer.modules.sequences.logic()
volumeSequenceBrowserNode = sequenceLogic.GetFirstBrowserNodeForSequenceNode(volumeSequenceNode)
sequenceLogic.UpdateProxyNodesFromSequences(volumeSequenceBrowserNode)

You can find more examples in the script repository.

To get started with Python scripting in Slicer, I would recommend the PerkLab Bootcamp Slicer programming tutorial.

5

Thanks for the link, you made my day.

1 Like
6

Agree, great answer by lassoan, thank you.

2 Likes
7

Yeah, I am glad I found this post.