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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Whenever you enter the automatic segmentation mode with some label X as the current drawing label, all the pixels already labelled X will be passed on to the automatic segmentation mode as initialization pixels.

ITK-SNAP Tutorial

What Additional Documentation tutoria, Available? 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.

If the image slices appear washed out, i. Click on the plus button in one of the four views to expand that view.

Underneath the VCR buttons is a control that allows you to set the size of the step used in snake evolution. In this tutorial, some sections are written for the expert users, and are optional.

The larger the step value, the fewer times will the user interface be updated as the snake evolves. It can be used to speed up large segmentations.

A three-button mouse with a scroll wheel is preferred, but is not necessary. Make sure that the label “caudates” is selected as the current drawing label Make sure that “All Labels” is selected snzp the Draw over snaap box.

ITK-SNAP 3.6 tutorial available online

This tab allows you to change the algorithm used for snake propagation. This information is improtant for contructing the feature image. At the top of the control panel is located a menu barwhich is used for saving and loading images, for setting options, and for accessing tutorisl help system.


This gives you a lot of creative control when segmenting multiple structures. We will use the 3D scalpel tool to assign different labels to the left and right caudate nuclei. A user who already uses a computer for image segmentation, and thus understands tutoriao fundamentals of three-dimensional medical imaging will be able to use SNAP after completing this tutorial. If you uncheck the Preview result checkbox, the slice windows will only reflect the values of the parameters when you press the Apply button.

These velocities are displayed using a fixed feature image, and not the feature image that you are working with. Step through the rest of the wizard, as descibed in Section 2. Hold down the left mouse button and drag the mouse towards the center of the image.

If SNAP has been installed on your system, consult your system administrator for instructions on starting it. Tiny bubbles will appear on the surface of the iti structure under the mouse.

Just check the box ‘Resample Region’ before pressing the Segment 3D button.

Reset Region and Segment 3D. 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. Simply select this tool, position the mouse over a rendered segmentation results e. Both the amount of memory and the time required to compete a segmentation can be reduces by selecting a sub-region of the image on which to perform segmentation. You may have noticed that the speed of segmentation in SNAP is roughly proportional to the size of the structure you are segmenting.

Use the History button to select the image loaded most recently. The information presented in this tutorial falls into the following categories: You can not save feature images in GIPL format because if does not support floating point voxels. Now that we’ve set the snake parameters, we are ready to run the snake evolution.


Using the clear label as the active drawing label, you can erase parts of the segmentation that have leaked outside of the caudates.

Otherwise, press the Accept button to repaint one of the caudates with the active drawing label and press the Update Mesh to see the result in 3D.

SNAP allows you to replace the standard four-view layout three slice views and a 3D view with a single-view layout. Check the Combined Display check box. Uncheck Combined Display check box to see the feature image again.

Tutorial: Getting Started with ITK-SnAP

The following window will appear. The draw over label functions the same way in automatic segmentation as in manual segmentation. The window displays dimensions of the image, voxel size, current cursor location and other useful information.

The first tutorkal is to take advantage of the option to resample the region of interest when entering the automatic segmentation mode. It does not affect the sign of the feature function at any particular voxel, but it does have an effect on the smoothness of the snake evolution. The red curve for which the velocities are shown can be changed using the mouse.

You can use this window to change the dimensions of the pixels that will be passed on to SNAP’s automatic segmentation mode. Press the Stop button when the caudates have been filled up Press the Rewind button if you want to restart.

This tutorial will refer to these panels as slice panels and the 3D panel.