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
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
- In Selected Label panel, name the description Ventricles.
- 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
- 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.