This short minute course was held at RSNA in Chicago on Nov 28 and Dec 1, The course offered a brief introduction to main. Segmentation steps using ITK SNAP semi-automatic segmentation based on Intensity Regions. From left to right, top: Definition of the region of interest.

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These are actions that the user should perform in the course of the tutorial, such as clicking on buttons and entering text. Uncheck Combined Display check box to see the feature image again. If the image slices appear washed out, i. In one of the slices position the mouse cursor near one of the corners of the selection box Hold down the ttorial mouse button and drag the mouse towards the center of the image. The Dense Level Itl Algorithm is included purely for experimental purposes.

Left-click once in one of the four windows showing tutoria curve and yellow ‘control points’ will appear. For instance, if the input image has 1x1x5 pixels, you can have SNAP replace each pixel by 5 isotropic ones, as shown above. SNAP allows you to replace the standard four-view layout three slice views and a 3D view with a single-view layout. We will now adjust the region of interest by dragging the sides of the selection box.

In this tutorial, we will use the term grey image to refer to the tktorial input image, e. The use of word region here should not be confused with region competition. Discard the Snnap Segmentation. It can also be used for tracing curves on the surface of anatomical structures, e. As an alternative to using bubbles, you can use manual segmentation to initialize the snake.

What Additional Documentation is Available? Now, something more complex. Press and hold the right mouse button and move the mouse up or down to zoom in and out in ikt 3D view Press and hold the middle mouse button and move the mouse to pan in the 3D view.

Now, we will use the 3D scalpel tool to actually draw a line in place of the imaginary line. In the semi-automatic mode, a powerful level set segmentation algorithm is used to segment anatomical structures in three dimensions. This section assumes that you are working with the image MRIcrop-orig.


ITK-SNAP Tutorial

This step of the wizard is used to position spherical bubbles to that initialize the snake, as described in the previous section. Move the crosshairs around in the slice windows the intensity region filter window will remain on top. The red curve for which the tutirial are shown can be changed using the mouse.

This tool is used to mark points on the surface of the 3D rendering of the segmentation results with the active drawing label. The automatic segmentation will be performed on the resampled image, and the results will be resampled back to the resolution of the original, anisotropic image. SNAP represents segmentation by assigning labels to pixels voxels in the input image. For example, if the original image has 1mm cube pixels and you resample it to 2x2x2 resolution, you will reduce the amount of memory needed for segmentation by eightfold and will speedup the segmentation by an eightfold as well.

Press the Accept button to relabel the pixels corresponding to these bubbles with the active drawing label, or press the Reset View to discard the spray painted bubbles.

In this step we will construct a region competition feature image appropriate for segmenting the caudate nuclei. You will find that the intensities in the caudate range between the high 40’s and low 60’s. This gives you a lot of creative control when segmenting multiple structures. Most of the SNAP window is occupied by four tutorail, three of which show orthogonal slices through an image, and the fourth, located at bottom left, shows the three-dimensional view of the segmentation.

Tuotrial bubbles will appear on the surface of the segmented structure under the mouse. Click on the plus button in the expanded view to collapse the view and display the other three views. Our goal in setting the parameters is to make sure that the voxels inside of fthe caudate nuclei are assigned positive values in the feature image, and that the voxels outside of it are assigned negative values.

Press and hold the middle mouse button and move the mouse to pan in the 3D view. The final step in the automatic segmentation process is to return to the SNAP manual segmentation mode, incorporating the segmentation results with other structures that have been previously segmented.


For brevity, only the most basic questions are answered here; more questions will be answered tutoril later sections rutorial the tutorial. SNAP provides a set of tools to make segmentation of volumetric data easier and faster. Now, let us examine the different tools available in the 3D Toolboxwhich is shown below.

ITK-SNAP 3.6 tutorial available online

You may have noticed that the speed of segmentation in SNAP is roughly proportional to the size of the structure you are segmenting.

Change the curvature velocity weight to from 0. The former tutoial used to reset the region of interest to the entire image. Select the 3D Scalpel Tool Click the left mouse button at one end of the imaginary line separating the caudates Move the mouse around the 3D window. Set the upper threshold to 63 Set the smoothness to 1. If your input device does not have a right tutoriwl a middle mouse button, use the following combinations keyboard mouse combinations:.

Use the Radius slider to change the radius of the bubble.

This section gives step by step instructions on segmenting an image using the region competition snake in last section’s terminology, snake evolution that uses the region feature image. You can, however, follow the general directions of this section using a different image, but you will have to use your own judgement in selecting various parameters.

This is information about SNAP that is necessary in order to use the tool. The size of the box will be adjusted as you move the mouse. Therefore, you can use the results of one segmentation attempt to initialize another. Next to the step size dropbox is a display that shows the current iteration. The window displays dimensions of the image, voxel size, current cursor location and other useful information.