Difference between revisions of "Examples"

Latest revision as of 21:04, 22 February 2012

Applying Face De-Identification, BSE, and Fuzzy C-Means

In this example, we will to show you how to record a script, and then run it in via the Scripting menu. The script includes:

1 Applying the Face De-Identification algorithm;
2 Applying the Extract Brain Surface (BET) algorithm;
3 And finally, performing brain segmentation using the Fuzzy C-Means > Single Channel algorithm.

Open an image of interest and then, press Start Recording Script button on the Scripts toolbar. The Record New Script dialog box appears indicating that recording a script is started.

Recording the Face De-Identification algorithm execution:
1 Call Algorithms > Brain Tools > Face De-Identification;
2 The Anonymize Face dialog box opens;
3 Fill out the dialog box as shown in Figure 19. The right column displays the script text corresponding to the dialog box options;
4 Press OK to run the algorithm.

After the algorithm finishes running and the result image appears on the screen, make the result image active and call the next Extract Brain Surface (BET) algorithm.

Recording the BET algorithm execution: 1 Call Algorithms > Brain Tools > Extract Brain Surface (BET);
2 The Extract Brain dialog box opens;
3 Fill out the dialog box as shown in Figure 20. The right column displays the part of the script corresponding to the dialog box options;
4 Press OK to start the algorithm.

After the algorithm finishes running and the result image appears on the screen, make the result image active and call the last algorithm - Fuzzy C-Means > Single Channel.

Recording the Fuzzy C-Means > Single Channel algorithm execution:
1 Call Algorithms > Segmentation > Fuzzy C-Means > Single Channel;
2 The Fuzzy C-Means dialog box opens;
3 Fill out the dialog box as shown in Figure 21. The right column displays the part of the script corresponding to the dialog box options;
4 Press OK to start the algorithm.

After the algorithm finishes running and the result image appears on the screen, close all intermediate images, and then save the final image.

Now, save the script. You might consider to add comments to the script text. In order to do that,
1 Click the Insert Comment icon located on the Record New Script dialog box toolbar;
2 The Enter Comment window appears;
3 Type in the comment and press OK;
4 The comment text appears in the Record New Script dialog box;
5 Save the script;
6 Close the dialog box.

To run the script via the Scripts menu
1 Call Scripts > Run Script from the main MIPAV menu;
2 Select the script you've just recorded, and press OK;
3 The MIPAV Script Tool dialog box opens;
4 In the dialog box, use the Add Images from File button to select and add images, on which you wish to run the script, to the Images window;
5 Then, use the mouse to drug images from the Images window to the Script Execution Setup window. Refer to Figure 22 and "Adding images to the Script Execution Setup";
6 Press Run Script.

The script starts running and the intermediate images and progress bars appear on the screen. See Figure 23.

When the algorithm finishes running, the progress bars disappear, and the results replace the original and intermediate images.

Script

The script text is shown below. Note that the comment strings included in the script start with "#".

Cloning images, adding margins, and applying gaussian blur

In this example, we will to show you how to record the script that does the following:
1 Clones an active image;
2 Adds margins to the clone;
3 Applies the Gaussian Blur algorithm to the clone, and produces the second clone;
4 Closes the original image and saves the clones.

To get started,

open an image of interest and then, press Start Recording Script button. The Record New Script dialog box appears indicating that recording a script is started, see Figure 24.

Here, ext_ indicates that this image is not produced within the script, but must be selected by a user.

Here, the command in the script is Clone. This command clones an image which is labeled as $image1 in the script, and then passes it as input_image_1 parameter to the Clone operator.

2 Now, select the clone image and call Utilities > Add Image Margins. In the Add Image Border dialog box, specify the margins as shown in Figure 25 and press OK.

This adds margins to the image clone1, and the following string appears in the Recording Script dialog:

Here, the command in the script is AddMargins(parameter1,...parameterN). Script parameters are as follows:

"input_image_1 image $image2" shows that the script applies to the active image clone

"do_output_new_image boolean false" indicates that the new image (with margins) appears in the same image frame replacing the old one[⁴]

"left_side int 20", "right_side int 20", "top_side int 20", "bottom_side int 20" are the image margins, refer to Figure 25

"front int 0", "back int 0" indicates that there are no slices added to the front and back of the image, refer to Figure 25

"margin_value double -5213.51513671875" - the margin fill value for grayscale images

"margin_value_rgb list_double 0.0,0.0,0.0" - the margin fill value for RGB images