Aligning Slices Manually
Tools to manually translate and rotate slices within a 3D image stack are provided in the Slice Registration contextual window whenever you work in Manual Registration mode. Translations and rotations can be applied to a single slice or to the remaining slices in the dataset.
In Manual mode, two image slices are displayed in the Preview window — the Reference slice and the Current slice. The Reference slice appears below the Current slice and cannot be modified. As you scroll through the dataset, the Reference and Current slices are updated so that you can apply translations and rotations as required throughout the dataset. You should note that only the first image in the stack cannot be modified.
Transformations can be implemented by either one of two mechanisms — at the input so that the original image data is transformed, or at the output so that a new dataset is created and the original image remains unmodified.
Manual mode
| Description | |
|---|---|
|
Color ramps |
Can be applied to the reference and/or current slices to help visualize differences between the slices. |
|
Fusion opacity |
You can change the opacity of the reference or current slices anywhere between 0% and 100%. |
|
Show |
Whenever Show is selected, the Translate and Rotate tools appear in the Preview window.
Refer to the topic Using the Move Tools for more additional information about the Translate and Rotate tools. |
|
Apply to subsequent slices |
If selected, changes will be applied to the Current slice and all slices remaining in the image stack. For example, if the Current slice is 50 in an image stack of 100, selecting this option will apply the transformation to slices 50 to 100 inclusively. If this option is not selected, changes will be applied only to the Current slice. |
|
Display lateral views |
If selected, shows the default layout of images. If not selected, a maximized view of the image plane will be shown. |
How to Align Slices Manually
- Right-click the required dataset in the Data Properties and Settings panel and then choose Dataset Slice Registration in the pop-up menu.
The Slices Registration contextual window appears. Registration controls are available in the panel on the left side, while images of the dataset are arranged in the workspace.
- Choose Manual in the Registration method in the drop-down list.
The Translate and Rotate tools appear in the image plane view.
- Scroll to the first image slice that you need to adjust.
You should note that adjustments are always applied to the Current slice in the Preview window.
- Select color ramps for the Reference and Current slices in the drop-down lists, optional.
You can also edit a color ramp, if required (see Using the LUT Editor).
Color ramps can help you to visualize differences in the displayed image slices.
- Adjust the opacity of the Reference slice, if required.
When the slider is at left, only the Reference slice will be visible. When the slider is at right, only the Current slice will be visible. When the slider is in the middle, the opacity of both slices will be at 50%.
- Check the Apply to subsequent slices option if want you adjustments to be applied to the Current slice and all other slices remaining in the image stack. If this option is not checked, changes will be applied to the Current slice only.
- Use the Translate and Rotate tools to manually correct the position and/or rotation of the Current slice (see Using the Move Tools).
If the Translate and Rotate tools are not visible in the Preview window, click the Show button.
- If required, you can click the Undo button to undo the current transformation.
- You can also reset slices in the dataset to a previous setting in the Registration(s) applied drop-down menu.
- Manually correct additional slices, if required.
- Save the registration, optional. See Saving and Loading Transformation Templates for information about saving transformations.
- Do one of the following:
- Choose the Transform current dataset option, if you want the registration to be applied directly to the original image data.
- Choose the Create new dataset option, if want to create a new dataset as the output of the registration process.
- Apply the registration to other datasets, optional (see Applying Transformations to Other Datasets).
- Click the OK button to complete the registration process.
See Exporting Images for information about saving modified or new datasets.
