SegRef3D

SliceBridge User Guide

SliceBridge is a web app that inserts blank slices between the contours in a NIfTI label map exported from SegRef3D. It creates anchor-slice data that can then be interpolated using 3D Slicerโ€™s Fill between slices effect.

๐ŸŒ‰ Open SliceBridge

๐Ÿ‘‰ SegRef3D SliceBridge

๐Ÿ‡ฏ๐Ÿ‡ต ๆ—ฅๆœฌ่ชž็‰ˆใฎไฝฟ็”จๆ–นๆณ•

Your files are never uploaded to a server. Reading, conversion, compression, and download all take place locally in your browser.

What this tool does

For example, suppose the original NIfTI has the following properties:

After conversion with SliceBridge, the output NIfTI will have:

The original label values, origin, orientation, and physical extent are preserved.

SliceBridge does not interpolate the anatomical shapes.

It prepares blank slices so that interpolation can be performed in 3D Slicer.

1. Export a NIfTI file from SegRef3D

After checking and editing the segmentation in SegRef3D, export the label map using Export NIfTI.

If you need the slice order reversed, use Export NIfTI (Reversed) in SegRef3D. SliceBridge preserves the orientation and origin stored in the input NIfTI.

2. Load the NIfTI file into SliceBridge

  1. Open SliceBridge.
  2. Drag and drop a .nii or .nii.gz file onto the page.
  3. Check the displayed image dimensions, voxel spacing, data type, and label values.

3. Configure the blank slices

Slice axis

In most cases, you can leave this set to ่‡ชๅ‹•ๅˆคๅฎš (Auto-detect). SliceBridge automatically selects the axis with the largest voxel spacing. You can also select the X, Y, or Z axis manually.

็ดฐๅˆ†ๅŒ–ๅ€็Ž‡ (Subdivision factor)

Specify how many intervals should be created from each original slice interval.

Check the displayed output spacing, image dimensions, and estimated data size.

4. Create the Anchor NIfTI

  1. Click Anchor NIfTIใ‚’ไฝœๆˆ (Create Anchor NIfTI).
  2. Wait until the progress reaches 100%.
  3. Click ใƒ€ใ‚ฆใƒณใƒญใƒผใƒ‰ (Download) to save the generated .nii.gz file.

Example output filename:

segref3d_labelmap_anchor_z0p65mm.nii.gz

5. Interpolate in 3D Slicer

5-1. Load the NIfTI as a Volume

  1. Open Add data in 3D Slicer.
  2. Select the .nii.gz file downloaded from SliceBridge.
  3. Set Description to Volume and load the file.

5-2. Open Segment Editor

  1. Open the Segment Editor module.
  2. Select the loaded NIfTI under Source volume.
  3. Click Add to create an empty segment.

5-3. Extract label value 1

  1. Select the new segment.
  2. Select the Threshold effect.
  3. Set both limits of Threshold Range to 1.00.
  4. Click Apply.

Only voxels with label value 1 are now assigned to the first segment.

5-4. Extract the other integer label values

Create a separate segment for each integer label value.

  1. Click Add again to create another empty segment.
  2. Select Threshold.
  3. For label value 2, set the range to 2.00โ€“2.00 and click Apply.
  4. For label value 3, add another segment, set the range to 3.00โ€“3.00, and click Apply.
  5. Repeat for every integer label value contained in the NIfTI.
Label 1: Add โ†’ Threshold โ†’ 1.00โ€“1.00 โ†’ Apply
Label 2: Add โ†’ Threshold โ†’ 2.00โ€“2.00 โ†’ Apply
Label 3: Add โ†’ Threshold โ†’ 3.00โ€“3.00 โ†’ Apply

You only need to create segments for the integer values listed under ใƒฉใƒ™ใƒซ (Labels) in SliceBridge. Rename the segments as needed, for example pelvis, obturator internus, and levator ani.

5-5. Interpolate all visible segments together

Fill between slices processes all segments whose eye icons are on, not only the segment highlighted in blue.

  1. Turn on the eye icon for every segment that you want to interpolate.
  2. Select Fill between slices.
  3. Click Initialize and inspect the preview for all visible segments.
  4. If the result is acceptable, click Apply once.
Show Segment_1, Segment_2, and Segment_3
โ†’ Fill between slices โ†’ Initialize once โ†’ Apply once

The visibility state determined by the eye icons controls which segments are processed. To interpolate only a subset, hide the other segments before clicking Initialize. This interpolation uses the segment shapes, not source volume intensities.

Notes

Unsupported data

Convert these datasets to a three-dimensional NIfTI-1 integer label map in 3D Slicer or another application before using SliceBridge.

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