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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

Manual registration settings
	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. Drag the Translate tool to move the current slice within the view. Use the Rotate tool to rotate the current slice from the pivot position. Refer to the topic Translating and Rotating Objects 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 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 Translating and Rotating Objects). 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 or more of the following to define the Output options:
- Select Transform current dataset, if you want the registration to be applied directly to the original image data, or Create new dataset, if want to create a new dataset as the output of the registration process.
- Select the Crop data to option, if required.
  You can crop the output to either the selection box used for the registration or to an adjustable used-defined box. These options are available in the drop-down menu.
- Select other datasets to which you want to apply the current registration to in the drop-down menu shown below, optional.
  Note Only equivalent datasets that have the same number of slices in the image stack will be shown in the drop-down menu.
Click the OK button to complete the registration process.
See Exporting Objects for information about saving modified or new datasets.