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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The crosshair position can be adjusted in this mode using the left mouse button as usual.

ITK-SNAP 3.6 tutorial available online

Underneath the VCR buttons is a control that allows you to set the size of the step used in snake evolution. You will need to use the Above threshold direction setting when creating the feature image. For brevity, only the most basic questions are answered here; more questions will be answered in later sections of the tutorial. You may have noticed that the speed of segmentation in SNAP is roughly proportional to the size of the structure you are segmenting.

Tips and tricks denoted by icon.

ITK-SNAP Tutorial

Reset Region and Segment 3D. The rest of the control panel houses a variety of buttons, sliders and other controls, which appear and disappear depending on the current mode of operation. The automatic segmentation component of SNAP requires a lot of computer resources. SNAP provides a set of tools to make segmentation of volumetric data easier and faster.

Try to simulate the selection box in the picture below. You will find that the intensities in the caudate range between the high 40’s and low 60’s.

Click the left mouse button again at the other end of the imaginary line. Cubic produces the best quality resampled images, but is slow. A user who already tutprial a computer for image segmentation, and thus understands the fundamentals of three-dimensional medical imaging will be able to use SNAP after completing this tutorial.

It can also be used for tracing curves on the surface of anatomical structures, e. The SNAP self-installer is available for download at http: If that were always the case, it would take a very long time to segment large structures such as the whole tutirial the brain white matter or gray matter.


Using all three slice windows, adjust the selection box to include the left and right caudate nuclei. After you use the mouse to click on and move the knobs that are used to change the threshold and smoothness values, you can use the left and right arrow keys to move these knobs one value at a time. Cubic interpolaion is recommended in most cases. In order to use the scalpel tool, we need to first rotate the 3D view such that a line can be drawn between the two caudates.

Move the crosshairs around in the slice windows the intensity region filter window will remain on top.

ITK-SNAP tutorial available online | PICSL

This tutorial is a walk-through of a SNAP segmentation session. In practice, it is possible to use a larger time step value, resulting in proportionally faster segmentations, but at a cost of sometimes unpredictable error. This tab also allows you to override the default time step used in snake propagation.

Set the upper threshold to 63 Set the smoothness to 1. The use of word region here should not be confused with region competition. If the selection box disappears in one of the slice windows, that means that the crosshairs position is outside of the selection box. The directions on obtaining and installing SNAP are available at http: This section contains a list of loosely organized list of SNAP features that can make it a more powerful tool than it may appear at first look.

In the semi-automatic mode, a powerful level set segmentation algorithm is used to segment anatomical structures in three dimensions. Use the History button to select the image loaded most recently. The Narrow Band algorithm is more robust with respect to increasing the segmentation time step see next paragraph. This step of the wizard is used to position spherical bubbles to that initialize the snake, as described in the previous section.

Check the Combined Display check box.


Press the Next button in the Segmentation Pipeline Wizard to proceed to the next step. SNAP can be used to segment a variety of three-dimensional images. As an alternative to using bubbles, you can use manual segmentation to initialize the snake. If your input device does not have a right or a middle mouse button, use the following combinations keyboard mouse combinations: The smoothness value determines the steepness of the mapping curve.

Try moving the curve and see how the foces change. In this step, we will select a subregion of the image that contains the caudate nucleus. This section also assumes that you are using the label file MRIcrop-seg. Make sure that the label “caudates” is selected as the current drawing label Make sure that “All Labels” is selected in the Draw over drop-down box.

Just check the box ‘Resample Region’ before pressing the Segment 3D button. The region of interest is a rectalinear box, while the regions in region competition are of arbitrary shape and are defined by uniform intensity. In order to perform the segmentation automatically, we will discard the manual segmetnation. The images have to be homogeneous, i.

The experimental noise reduction option can be used in conjunction with overriding the optimal time step. The default setting is to use the so-called optimal time step: SNAP does not require a deep understanding of the underlying mathematics and computer science to use.

The segmentation labels on one side of the plane are replaced by the current drawing label, as long as they agree with the current setting of the draw over label. Press and hold the right mouse button and move the mouse up or down to zoom in and out in the 3D view Press and hold the middle mouse button and move the mouse to pan in the 3D view.