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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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. You will see a white line indicating where the ‘cut’ will be made, and an arrow indicating which half of the space sanp be relabeled.

ITK-SNAP 3.6 tutorial available online

Press the Add Bubble button to place a bubble at the crosshairs position. This window consists of two parts.

The option to resample an image has been added to SNAP especially for turorial with such images. This tutorial is a walk-through of a SNAP segmentation session. Position the mouse over any point on the caudates and click the left mouse tutofial. Once you have adjusted the region of interest, press the Segment 3D button.

Press the Step button several times to run the snake for a few iterations Press the Run button once and watch the snake fill up the caudates. If your input device does not have a right or a middle mouse button, use the following combinations keyboard mouse combinations:. Nearest neighbor interpolation is fast but results in greatest distortion. Move the crosshairs around the caudate nuclei. Be aware, however, that supersampling an image in this way increases memory usage fivefold in this caseand should be done only for small regions of interest.

It is up to the user to come up with the list of labels to use in a particular segmentation task. For brevity, only the most basic questions are answered here; more questions will be answered in later sections of the tutorial. Left-click once in one of the four windows tutoriaal the curve and yellow ‘control points’ will appear.


The left portion of the SNAP window is occupied by a tall ihk area called the control panel. This tool tutoriql used to mark points on the surface of the 3D rendering of the segmentation results with the active drawing label. 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.

The draw over label functions the same way in automatic segmentation as in manual segmentation. Action items denoted by icon. In this step we will construct a region competition feature image appropriate for segmenting the caudate nuclei. In this tutorial, we itj use the turorial grey image to refer to the three-dimensional input image, e. In addition to the main window shown above, several other windows will pop-up during the SNAP session.

It can also be used for tracing curves on the surface of anatomical structures, e. Now that we’ve set the snake parameters, we are ready to run the snake evolution.

Tutorial: Getting Started with ITK-SnAP

The window displays dimensions of the image, voxel size, current cursor location and other useful information. The manual mode is used for segmentation using hand contouring and for cleaning up the results of automatic segmentation. If SNAP has been installed on your system, consult your system administrator for instructions on ttuorial it. Otherwise, press itj Accept button to repaint one of the caudates with the active drawing label and press the Update Mesh to see the result in 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 first way is to take advantage of the option to resample the region of interest when entering the automatic segmentation mode. As you change the parameters, the slice windows are updated immideately. Use the procedure outlined in the steps above to segment the ventricles in the image.


Click below to jump to a specific tip:. Discard the Previous Segmentation.

ITK-SNAP Tutorial

The snake evolution algorithms used in SNAP are poorly suited for non-isotropic images, especially wen anisotropy is great, e. Look tutorual the values of the feature image, which are reported in a box labeled “Preproc” underneath the toolbar.

Obtaining, building and running SNAP as part of this distribution requires considerable knowledge of system administration and computer programming. SNAP represents segmentation by assigning labels to pixels voxels in the input image.

This is additional, often mathematical information for advanced users. Select ‘right caudate’ as the current drawing label, and select ‘caudates’ the label used for automatic segmentation as the label to draw over, as shown below. tutoial

This information is improtant for contructing the igk image. In this tutorial, automatic segmentations were initialized using ‘bubbles’.

Most of the SNAP window is occupied by four panels, three of which show orthogonal slices through an image, and the fourth, located at bottom left, shows the itkk view of the segmentation. The following window will appear. You can also load feature images by pressing the Load from File The information presented in this tutorial falls into the following categories:.

Set the lower threshold to Reset Region and Segment 3D.

Simply select this tool, position the mouse over a rendered segmentation results e. The selection box displays the region of interest that will be used in automatic segmentation. A user who already uses a tutorixl for image segmentation, and thus understands the fundamentals of three-dimensional medical imaging will be able to use SNAP after completing this tutorial.

Click the left mouse button at one end of the imaginary line separating the caudates. You can also use manual segmentation tools to construct the snake initialization.

Luckily, SNAP provides a couple of ways to speed up large segmentations.