Software at CIS : BrainWorks: Tutorials: Landmarking
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Overview
This tutorial walks the user through the steps of generating landmark data and volumes using BrainWorks software.
Start Brainworks program using command line bwnew&.
The Load Surface dialog is displayed.
Navigate to the directory containing the surface data (byu) files. The files in the directory are listed on the right side of the screen.
To select a file, highlight the file using the left mouse button, then select the OK button.
The Load Surface dialog is displayed. Select the Load button. The surface data is now loaded into BrainWorks.
Select Surface from the Menu. A drop down menu is displayed. Select Landmarking from the drop down menu.
The surface data is displayed graphically.
To place landmarks on the image the middle mouse button is used. If your mouse does not have three mouse buttons located towards the front of the mouse, the third mouse button may be located on the left side of the mouse (used by the thumb). The order that landmarks are chosen is important. This order must be consistent among images that will be compared with one another. In this example of hippocampus data, the first landmark will be placed on the head of the hippocampus. Move the mouse to the desired area and press the middle mouse button.
The landmark is displayed on the image and the landmark name "no-name" is displayed to the right of the image. To name the landmark "L1" highlight the name with the mouse and type "L1". Should the user wish to change the location of a landmark, the user selects the "Change Current" button on the right hand sign of the screen using the left mouse button. Any subsequent press of the middle mouse button will reposition the landmark. When the user is satisfied with the position of the landmark the user selects the "Change Current" button with the left mouse button. Subsequent presses of the middle mouse button will result in new landmarks.
It is not necessary to rename a landmark as soon as it is added. Add other landmarks to the image (in this example five new landmarks will be added before being renamed). As stated previously, it is important to be consistent in the order landmarks are added for images that will be compared to one another. As landmarks are added, the color of the previous landmarks changes to blue, the most recently added landmark is displayed red.
The subsequent landmarks can all be renamed by highlighting each name and entering the appropriate text. After landmarks have been named save landmark data. To save landmark data, select the "Save LMK" button on the right hand side of the screen.
The Save Landmarks As dialog is displayed.
Enter the file name in the Selection edit box at the bottom of the screen. Select OK.
Close the image window by selecting the X in the upper right corner of the window.
The initial BrainWorks window is displayed.
Select Surface from the Menu. A drop down menu is displayed. Select Modify from the drop down menu.
Select Modify from the Menu. The modify menu is displayed. Select Scale To from the menu.
The Scale To dialog is displayed. The values Center X, Center Y and Center Z need to be modified depending on the size of the image. For example if an image is 80 x 96 x 80 enter Center X = 40, Center Y = 48 and Center Z = 40. The values entered must equal the midpoint of the image dimensions. To enter the value highlight the value in the edit box with the mouse and type new value.
The initial BrainWorks window is displayed.
Select Surface from the Menu. A drop down menu is displayed.
Select Closed Filled Volume Mask. The Binary Seg dialog is displayed.
Enter the dimensions of the image in the Img fields. For example if image has dimensions 80 x 96 x 80 enter Img NX = 80, Img NY = 96, Img NZ = 80.
The volume has now been created.
Move the mouse over the volume on the left side of the screen. Right click the mouse. A pop up menu is displayed. Select Save.
The Save Image dialog is displayed.
Select the File button on the Save Image Dialog. The Select Volume dialog is displayed.
Enter file name for image (include .img suffix) in the Selection edit box. Select OK button.
Select Save button on Save Image dialog.
Last Modified: Monday, 25th April, 2011 @ 11:19am
