Segmentation

Contents

  1. Segmentation
    1. Description
    2. Create an image stack for use with ITK-Snap
    3. Segmentation with ITK-Snap 3.0

Description

Here you will learn how to make a segmentation from CT scan through ITK-snap. This segmentation will allow you to construct your mesh later on Blender. From the CT scan, you have to distinguish the myocardium and reconstruct it on ITK-snap.

Create an image stack for use with ITK-Snap

  • One option is to use ImageJ to create an image stack

  • File->Import->Image Sequence (import any types of image files)

  • A good image sequence generally have the quality of the one showed below.

  • File->Save as->Analyze 7.5 (one format used by ITK-Snap), with the extension “.hdr”, example: Segmentation.hdr

Segmentation with ITK-Snap 3.0

  • File->Open Image…

  • Open Segmentation.nii . Choose NiFTI for image file format. You can also load DICOM, Raw binary, Metaimage and Analyze format files on ITK-Snap. More tutorials on ITK-Snap can be found on http://www.itksnap.org/pmwiki/pmwiki.php?n=Main.HomePage

  • Tool->Label Editor…

    • In Selected Label panel, name the description Ventricles.

    • Click Close.

  • Select the snake tool in the main toolbox

  • As you select the snake tool, a pink-colored dashed selection box will appear at the border of the each slice in the slice windows.
  • Move the dashed line to select your segmentation part.

  • Click Segment 3D to start Automatic Segmentation.

  • Segment 3D Step1 of 3. Action A: choose Region competition.

  • Actions B: Reprocess -> Speed Image Generation…

    • Thresholding: Lower threshold~700; Higher threshold ~1800; Smoothness between 1.00 and 2.00.
    • Threshold directed: Two sided.
    • Live preview: Blue-White.
    • Click Apply and OK.

  • Action C: Next…

  • Step2/3: Initialization. Move the crosshairs such that the crosshairs position is inside of the ventricle walls in all three slice windows. Press the Add Bubble button to place a bubble at the crosshairs position. Use the Radius slider to change the radius of the bubble.

  • Action C: Press next.

  • Step 3/3. Action A: Set Parameters…

    • Region competition force 1.0, smoothing force 1.2
    • Close
  • Action B: Execute and control evolution

    • Click  several times to run the snake for a few iterations.

    • Click  once and watch the snake fill up the ventricle walls.

  • Action C: Click Finish when then ventricle walls have been filled up.

  • Press the Update Mesh Button below the 3D window and render the results. The results of the segmentation should look something like this.

  • Segmentation -> Export as Surface Mesh. Export a mesh for a single label. Choose STL mesh file for mesh file format. Name the file e.g. Seg.stl

  • Note, if you want to save your segmentation and come back later, Segmentation-> Save as image. Save it with the extension “.mhd” (metalmage file), example: Segmentation.mhd. To load it after, Segmentation -> Load from image.