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Using ITK-SNAP

Installation and use of ITK-SNAP (all platforms)

ITK-SNAP is a visualization software available on major platforms (Windows, macOS and Linux).

Download here: http://www.itksnap.org/pmwiki/pmwiki.php?n=Downloads.SNAP3

Select the latest version corresponding to your platform.

Load and view MR images

When first opening ITK-SNAP, you will be presented with the following screen.

To open the first image, select "File > Open Main Image".

The dialog box "Open Image -- ITK-SNAP" will open. Click on "Browse" to search for the file you want to load (load the T1-weighted image at this stage).

Once you click "Open", the following dialog box will appear:

Click "Next". The image will be loaded, and a final dialog box with the image characteristics will be displayed. Click on "Finish".

ITK-SNAP allows juxtaposition of multiple images. To add a new image, select "File > Add Another Image ...".

The same dialog box presented earlier will appear. We recommend loading the T2-weighted file. Until the selection of the image, the procedure is exactly the same.

When clicking "Next", ITK-SNAP will ask to display the additional image as a separate image, or as an overlay. Choose "As a separate image (shown beside other images)". Click "Next", and a dialog box summarizing the additional image's properties will appear. Click on "Finish" to proceed.

Notice that both images are not juxtaposed next to one another.

To enable this display, click the button highlighted in red as follows.

To explore one orientation more closely, you can extend its view to full screen by clicking one of the highlighted red buttons.

This will result in the following display (when axial view is selected).

Re-click the same button to revert to the original view.

Repeat the procedure of adding additional images for relative intensity and gradient.

Adjusting image color and contrast

Select "Tools > Image Contrast/Contrast Adjustment...".

The following dialog box will appear:

First, select the "Color Map" panel. Then, select relative intensity in the left panel.

Next, click on "Select a colormap" and select "Hot".

Repeat this for the gradient image. The viewer should now be organized as illustrated below.

Next, access the "Contrast" Panel. To adjust the contrast of the relative intensity image, you can slide the point (solid yellow dot) situated on the left of the intensity histogram to the right.

Conversely, slide the point on the right of the intensity histogram towards the left to adjust the gradient contrast.

Your images are now ready to be reviewed.

Important points when evaluating a case

The textures pipeline should be used only when a FCD Type II is suspected. It is NOT recommended to use this pipeline for the detection of any other epileptogenic lesions, such as hippocampal sclerosis, heterotopias or tumors.

The output images of the pipeline include: 1) T1 2) FLAIR 3) gradient magnitude map (modeling blurring: darker regions compared to the surroundings), and 4) relative intensity map (showing the hyperintensity of the FCD relative to the rest of the brain GM and WM)

Maps do not show only changes related to the FCD. The relative intensity maps display hyperintensities in other brain regions (including the central areas, insula, mesiotemporal lobe, the basal ganglia and thalamus), due to biological reasons other than the presence of an FCD. Detection of an FCD in these areas are more difficult.

On the gradient magnitude map, the contour of the ventricles appears as a bright signal because of the strong contrast between WM and CSF.

FCD Type II lesions are typically characterized by the co-occurrence of blurring (dark cortex on gradient map) and hyperintensities (on relative intensity map).

In general, any lesion highlighted on texture maps should be visible on conventional T1 and FLAIR images.