Difference between revisions of "Select Algorithms and Brain Tools for Talairach Transform"

Note: If you need to erase a landmark point that you've already set, select the point in the image. Return to the Create AC-PC Image dialog box and select the radio button for the point you want to delete. For example, to delete the AC posterior margin, select that radio button. Then click Clear (the Clear button only becomes available when you've completed the preceding instructions correctly).
17 Return to the Create AC-PC Image dialog box (Figure 11) when all landmark points are marked, and click Apply.

Tip: The Apply button only becomes available when all of the landmark points are correctly selected and set. A point is correctly set when the settings you chose appear to the right of each point (Figure 11).
A progress message appears, and then the image produced from the settings you specified appears in a new image window. The result is an AC-PC aligned image (Figure 13]).

18 Refresh the list of images in New image to transform. The transformed image, whose title is the name of the original image followed by _acpc, appears in the list (Figure 12).

Note: The slice of the AC-PC image that displays may differ from the slice shown in the original image. By default, the AC-PC image appears at its center slice.
You may now want to save the AC-PC transform. If somehow you are interrupted in the procedure of transforming a brain image into Talairach space, saving the transform prevents your having to perform AC-PC alignment again.

To save the AC-PC transform (recommended) 1 Click Save in the Talairach Transform dialog box. The Save Talairach Transform File dialog box (Figure 14) opens.
2 Navigate to the directory in which you want to save the transform.

4 Click Save. MIPAV saves the AC-PC transform to the folder you specified.

5 Type the file name for the transform and the extension.
Note: The AC-PC transform file is a text document that can be read with any text editor, such as Microsoft Notepad.
6 Click Save. MIPAV saves the AC-PC transform to the folder you specified.

To resolve errors

An error may occur if there is a 2-percent angular difference between the planes defined by AC-PC-MS1 and AC-PC-MS2. To resolve it, the ideal way is to align perfectly the MS1 and MS2 points on the midsagittal plane: using well-defined planes (choosing MS1 and MS2 far from the AC-PC line, one rather on the front and one on the back of the brain). If that fails, there is still the much less reliable method to have both MS points close to each other, so they define about the same plane.

To view the AC-PC settings for the AC-PC transformed image
1 Select the AC-PC transformed image that you just created.
2 Select Image > Attributes > Edit Attributes. The Image Attributes dialog box opens.
3 Click Talairach. The Talairach page appears.
4 Enlarge the Image Attributes dialog box (Figure 16) to show all of the fields in the dialog box.
Now that you have performed the AC-PC transformation on the image, the settings appear in the AC-PC group. However, because you have not yet performed the Talairach transformation on the image, the settings for the fields in the Talairach group still remain "1.0".
5 Click Close. The Image Attributes dialog box closes.

To load a previously saved AC-PC transform
1 Open the original image of the brain on which you performed AC-PC alignment.
2 Select Plug-Ins > Algorithms > TalairachTransform. The Talairach Transform dialog box opens.
3 Select the name of the original image in New image to transform.
4 Select acpc to orig. in Transformation.
5 Click Load. The Load Talairach Transform File dialog box opens.
6 Navigate to the directory in which you saved the AC-PC .txt file and select the file.
7 Click Open. A message appears on the Data page in the Outlook window saying that "transform data loaded from <path>."
8 Click Compute. A progress message appears, and then the image produced from the loaded AC-PC transform appears in a new image window. The result is an AC-PC aligned image.

Performing Talairach alignment

The AC-PC image that was generated now needs to be aligned in the Talairach coordinate system. Talairach alignment consists in scaling the brain to match its boundaries with those of the Talairach atlas. It is a 12 degrees of freedom, piece wise linear transform. It brings the AC, PC, and anterior, posterior, left, right, inferior, and superior boundaries of the brain to normalized positions (Figure 17).

After the AC-PC image is generated, it is necessary to find the six most anterior, posterior, left, right, inferior, and superior points, or, alternatively, the bounding box enclosing the brain. These points, along with the AC-PC landmark points, define a set of 12 boxes. In each box independently, the image is scaled along the three dimensions of the Talairach coordinates. Continuity is guaranteed since the boxes share common faces.

Talairach alignment is nonlinear as it scales differently the 12 boxes. Any direct measurement in this coordinate system is irrelevant: voxels have a different resolution in different boxes. For this reason, it is important to have the ability to bring back any Talairach-aligned image into the original image or the AC-PC aligned coordinates.

To perform Talairach alignment
1 Select the AC-PC image in New image to transform box in the Talairach Transform dialog box (Figure 18).
2 Select Talairach. The Create Talairach Image dialog box (Figure 19) appears on top of a triplanar view of the AC-PC image.
Tip: The goal at this point is to mark the limits of the brain: most anterior, most posterior, most superior, most inferior, most left, and most right points. The exact location of the points is not important as long as they bound the cerebrum.
3 Select Most anterior point in the Create Talairach Image dialog box.
4 Go to the triplanar view of the image. Select the point that is the most anterior point in the image. The important information is the position of the green line.
5 Click Set in the Create Talairach Image dialog box.
6 Repeat this procedure for the remaining points. When you finish setting the points, the Apply button becomes available.

7 Click Apply. A status message appears during processing. When processing is complete, the Talairach aligned image (Figure 20) appears.
8 Click the Refresh button to refresh the list of images in New image to transform. The transformed image, whose title is the name of the original image followed by _acpc_Tlrc, appears in the list (Figure 21).
At this point, you may want to save the Talairach transform. Doing so eliminates the need to repeat the Talairach process for this dataset. If interruptions at this point prevent you from completing tasks 2 through 6, saving the transform allows you to resume where you left off.
Note: You can use the Talairach transformation to bring other co-registered images into Talairach space and to send atlas information into the original image space.

To save the Talairach transform (recommended)
1 Select the Talairach-aligned image that was generated.
2 Click Save in the Talairach Transform dialog box. The Save Talairach Transform File dialog box (Figure 14) opens.
3 Navigate to the directory in which you want to save the transform.
4 Type the file name for the transform and the extension .txt.
5 Click Save. The Talairach transform is saved in the folder you specified.
Note: The Talairach transform file is a text document that can be read with any text editor, such as Microsoft Notepad.

To view the Talairach settings for the Talairach-transformed image
1 Select the Talairach-transformed image.
2 Select Image > Attributes > Edit Attributes in the MIPAV window. The Image Attributes dialog box opens.
3 Click Talairach. The Talairach page appears.
4 Enlarge the Image Attributes dialog box (Figure 23) to show all of the fields in the dialog box.
The settings in the Talairach group should now reflect the settings for the Talairach-transformed image. The Talairach page should also still show the settings for the AC-PC transformed image.
5 Click Close. The Image Attributes dialog box closes.

Task 2, Applying Talairach VOIs