New feature: Thick slab reconstruction from slice controllers and views

Sam_Horvath · October 26, 2023, 7:33pm

Thick slab reconstruction (TSR) can now be enabled and modified from the slice controllers and slice views!

Enabling thick slab reconstruction as well as selection of the composite method (min, max, mean or sum) has been available through the python console.

Now these options are available through both the slice controller and the right-click context menu on the slice views. If the interactive option is selected, the thickness, angle and position of the TSR can be adjusted by moving the slice intersections in the slice views.

Slice Controller (Default)	Slice Controller (Slab Enabled)	Slice Controller (Slab Enabled + Interactive)

Slice Viewer (Handle Interaction )	Slice Viewer (Right-click context menu)	Slice Viewer (slice intersection & Slab & Interactive)	Slice Viewer (Red & Yellow Slab enabled then Linked)

These features are currently available in the preview version of 3D Slicer.

Issue 1, PR 1 (slice controller implementation)
Issue 2, PR 2 (slice views implementation)

Melodicpinpon · February 16, 2024, 12:25pm

This slice controller is a very good news!
How can I use it?

jcfr · February 16, 2024, 2:01pm

After installing Slicer, are you able to enable “Thick Slab Reconstruction” from the Slicer controller ?

AlexZivelonghi · July 17, 2024, 11:06am

Hello, this is a great feature. Is there a way to remove slabs before exporting a snapshot ? It would be really great, since some details can be hided from the slabs

mohammed_alshakhas · July 17, 2024, 6:57pm

can i create a lateral cephalometry from skull ct with thick slab ?

ZhsChen · February 11, 2025, 9:20am

Hi, very useful tool! Thanks.
However, the slab thickness seems to not work correctly on my data. As you can see in the capture below, the two red lines already cover the whole volume, but the MIP image in the Red view does not really show all vessels. If I increase the interval between the two red lines, more vessels will appear on the MIP image. Do you know why? And how to fix it?

pieper · February 11, 2025, 12:55pm

@ZhsChen can you share the data or reproduce on public data?

ZhsChen · February 11, 2025, 1:43pm

Hi Pieper, I just tried on the DZ-MR_1 data in the sample dataset CBCT-MR Head, same problem occurred. In the two captures below, the projection slabes both cover the whole head, but the MIP images are different.

pieper · February 11, 2025, 2:14pm

Can you explain why you think the MIP is incorrect?

ZhsChen · February 11, 2025, 2:31pm

In the two captures above, I expect the two MIPs (in the Red view) to be exactly the same, since in both images the projection slab covers the whole head (the region outside the head has zero or very low value, and will not be projected to the MIPs).

ZhsChen · February 11, 2025, 2:35pm

But they are different. This suggests that the real slab used for projection is smaller than the slab between the two red lines.

lassoan · February 11, 2025, 3:58pm

This is the code that sets up thick slab reslicing parameters:

github.com/Slicer/Slicer

Libs/MRML/Logic/vtkMRMLSliceLogic.cxx

05e03affb


      
          void vtkMRMLSliceLogic::UpdateReconstructionSlab(vtkMRMLSliceLogic* sliceLogic, vtkMRMLSliceLayerLogic* sliceLayerLogic)
          {
            if (!sliceLogic || !sliceLayerLogic || !sliceLogic->GetSliceNode() || !sliceLayerLogic->GetSliceNode())
            {
              return;
            }
          
            vtkImageReslice* reslice = sliceLayerLogic->GetReslice();
            vtkMRMLSliceNode* sliceNode = sliceLayerLogic->GetSliceNode();
          
            double sliceSpacing;
            if (sliceNode->GetSliceSpacingMode() == vtkMRMLSliceNode::PrescribedSliceSpacingMode)
            {
              sliceSpacing = sliceNode->GetPrescribedSliceSpacing()[2];
            }
            else
            {
              sliceSpacing = sliceLogic->GetLowestVolumeSliceSpacing()[2];
            }

This file has been truncated. show original

Most likely the slabNumberOfSlices and slabSliceSpacingFraction computation has to be fixed.

Antmaker · April 17, 2026, 11:18pm

I am able to replicate this behavior on Slicer v.5.10.0 on Linux and am trying to understand this behavior.

Due to my limited understanding of how 3D Slicer works, I am thinking this is more of my ignorance instead of anything needing fixing.

Could the masters point me in the right direction?

Use Case

I have a masked scalar volume that I got by using the Mask Scalar Volume module. Now, I am trying to get the Max Intensity Projection (MIP) in coronal view.
However, I am seeing the same behavior as New feature: Thick slab reconstruction from slice controllers and views - #9 by ZhsChen.

Questions

What is “prescribed slice spacing?” The 3D Slicer Documentation nor Github source search revealed anything informative unfortunately.

github.com/Slicer/Slicer

Libs/MRML/Logic/vtkMRMLSliceLogic.cxx

05e03affb


      
          {
            return;
          }
          
          vtkImageReslice* reslice = sliceLayerLogic->GetReslice();
          vtkMRMLSliceNode* sliceNode = sliceLayerLogic->GetSliceNode();
          
          double sliceSpacing;
          if (sliceNode->GetSliceSpacingMode() == vtkMRMLSliceNode::PrescribedSliceSpacingMode)
          {
            sliceSpacing = sliceNode->GetPrescribedSliceSpacing()[2];
          }
          else
          {
            sliceSpacing = sliceLogic->GetLowestVolumeSliceSpacing()[2];
          }
          
          int slabNumberOfSlices = 1;
          if (sliceNode->GetSlabReconstructionEnabled()
              && sliceSpacing > 0
              && sliceNode->GetSlabReconstructionThickness() > sliceSpacing

The “slice spacing” the getter is getting is the thickness of each slice, thus it is the diff of the mm change as I scroll through the slice viewports.

github.com/Slicer/Slicer

Libs/MRML/Logic/vtkMRMLSliceLogic.cxx

05e03affb


      
          vtkImageReslice* reslice = sliceLayerLogic->GetReslice();
          vtkMRMLSliceNode* sliceNode = sliceLayerLogic->GetSliceNode();
          
          double sliceSpacing;
          if (sliceNode->GetSliceSpacingMode() == vtkMRMLSliceNode::PrescribedSliceSpacingMode)
          {
            sliceSpacing = sliceNode->GetPrescribedSliceSpacing()[2];
          }
          else
          {
            sliceSpacing = sliceLogic->GetLowestVolumeSliceSpacing()[2];
          }
          
          int slabNumberOfSlices = 1;
          if (sliceNode->GetSlabReconstructionEnabled()
              && sliceSpacing > 0
              && sliceNode->GetSlabReconstructionThickness() > sliceSpacing
              )
          {
            slabNumberOfSlices = static_cast<int>(sliceNode->GetSlabReconstructionThickness() / sliceSpacing);
          }

The SlabReconstructionOversamplingFactor is something similar to “Oversampling factor” under Segmentation geometry of the Segment Editor module? 3D Slicer Documentation also did not specify what this attribute that the getter is getting mean.

github.com/Slicer/Slicer

Libs/MRML/Logic/vtkMRMLSliceLogic.cxx

05e03affb


      
                && sliceSpacing > 0
                && sliceNode->GetSlabReconstructionThickness() > sliceSpacing
                )
            {
              slabNumberOfSlices = static_cast<int>(sliceNode->GetSlabReconstructionThickness() / sliceSpacing);
            }
            reslice->SetSlabNumberOfSlices(slabNumberOfSlices);
          
            reslice->SetSlabMode(sliceNode->GetSlabReconstructionType());
          
            double slabSliceSpacingFraction = sliceSpacing / sliceNode->GetSlabReconstructionOversamplingFactor();
            reslice->SetSlabSliceSpacingFraction(slabSliceSpacingFraction);
          }
          
          //----------------------------------------------------------------------------
          void vtkMRMLSliceLogic::UpdatePipeline()
          {
            int modified = 0;
            if ( this->SliceCompositeNode )
            {
              // get the background and foreground image data from the layers

Topic		Replies	Views
Thick slab reconstruction and maximum/minimum intensity volume projections Support	2	227	April 15, 2026
Slice thickness Support	5	1739	December 28, 2023
2D MIP (maximum intensity projection) not works in Slicer 5.6.1 Support	4	361	April 15, 2026
Thick slab reconstruction does not work with MicroCT Development volume , gui	2	75	September 11, 2024
Reset Slice view after Maximum intensity projection or Thick slab reconstruction Support	1	490	December 25, 2020

New feature: Thick slab reconstruction from slice controllers and views

Use Case

Questions

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