Reorientation Tool

The Reorientation Tool enables realignment of image data via translation, rotation, or flipping. Reference and input data may be manipulated separately and specific translation settings may be saved/loaded for future studies, including the option for setting automatically applied default SPECT shifts.

Getting There

The Reorientation Tool can be accessed via the tool pull-down menu on the IVS front panel.

Using the tool

When the Reorientation tool is selected a Reorientation window is displayed. Here, there is an option to highlight the Reference or input study (or both) for reorientation by ticking the boxes beside them. The images can be rotated up to 360 degrees around their X, Y and Z axis or translated in any direction along their X, Y and Z axis. To manipulate data sets under the management of the Data Manager use the Trans Input* option from the Operations menu.

Rotation is completed by either moving the arrow in the appropriate circle or else typing in the number of degrees you wish to rotate the image in the box underneath the circle. Once the desired positioning has been achieved, OK is pressed to update the reorientation.
Translation is achieved by scrolling the bar to the left or the right or typing in the number of mm to be moved in the box below. Once the desired positioning has been achieved, OK is pressed to update the reorientation.
Reset can be selected to return the image back to its original orientation.

Menu Options

File

The Reorientation File menu can be used for storing transformations, setting a default SPECT transformation, and controlling the window.

Load Transformation...	Ctrl+Shift+L	Applies a pre-defined transformation to the active data set.
Save Transformation...	Ctrl+Shift+S	Saves the current transformation settings (rotation, translation, flips) into a .xml file.
Save as default		Saves the current transformation settings (rotation, translation, flips) as default settings for SPECT data. If the "Apply Default Shift" checkbox is selected, these settings will be automatically applied to any SPECT data that then gets loaded. See the How To Guide for more on setting a default SPECT shift.
Reset	Ctrl+R	Resets all transformation settings (rotation, translation, flips) back to the default values.
Apply	Ctrl+Return	Applies the current transformation settings (rotation, translation, flips) to the active data set.
Close	Ctrl+Q	Closes the Reorientation window without applying any transformations to the data.

Operations

The Reorientation Operations menu can be used for selecting axes, performing flips, generating a quick preview, and enabling advanced options.

Fixed Trans. Axes		Fixes the active axis during transformation. For example, performing a z-axis Translation with this option selected, fixes the view of the transverse slice. Unselecting the option results in a transverse view that changes as the object is shifted. The view along the other two axes is not affected.
Trans. Reference	Ctrl+0	Toggles the transformation status of the Reference data. This option is linked to the checkbox on the main Reorientation panel.
Trans. input 1	Ctrl+1	Toggles the transformation status of input 1. This option is linked to the checkbox on the main Reorientation panel.
Trans. input 2	Ctrl+2	Toggles the transformation status of input 2. This option is linked to the checkbox on the main Reorientation panel.
Trans. Input*		Toggles the transformation status of all data sets under the management of the Data Manager.
Flips		Provides the option of flipping the data in any of three directions, described as Head/Feet, Left/Right, and Anterior/Posterior.
Quick Preview		This function is useful for large data sets that are slow to fully re-orient. Using Quick Preview gives a lower image quality preview of how the object will appear following Reorientation.
Advanced Options - Scaling		Use scaling to change the size of an image in any of the three directions. Hold down the shift key while engaging a slider bar to enable homogeneous scaling.
Advanced Options - NNB Interpolation		When manipulating atlases and other integer-only data sets, linear interpolation may be detrimental. Use the Nearest-Neighbor (NNB) Interpolation option to preserve integer values upon transformation.

How to Set a Default SPECT Shift

One of the most powerful features of the NanoSPECT is its ability to automatically register SPECT and CT data to create anatomically and functionally valuable fused images. Imaging without the application of any transformation typically results in data that are fused well within 1.5mm in any direction. However, taking the time to set up a default SPECT shift can help insure that all image acquisitions are perfectly fused.

Make a simple phantom, but one that breaks symmetry along multiple directions. A syringe with an air bubble, placed in the bed at an angle works well.

Collect a SPECT/CT of the phantom. It is recommended that standard reconstructions (or better) are used for both the SPECT and the CT to enable more precise transformation settings.

Uncheck the "Apply Default Shift" box located in the DICOM browser.

Load the data into the IVS.

Use the reorientation tool to shift and/or rotate the SPECT data set (Input 1) so that the SPECT and CT data are perfectly aligned. Typically, only shifts are needed for this operation. If rotations are needed, they should be only plus/minus 1 degree.

Before hitting "Apply", go to File | Save As Default and save the transformation

Return to the DICOM Browser or go to the Tools Menu and re-check the "Apply Default Shift" box.

Reload the SPECT/CT phantom data that were just acquired. They -- and all other data sets -- will now be perfectly fused

NOTE: This same formalism may be used to generate other Transformation files. Instead of choosing "Save as Default" in the Reorientation File Menu, choose "Save Transformation." Then it is possible to later load that transformation (using the "Load Transformation" option in the Reorientation File menu). These saved transformations are useful when fusing data from other modailities with NanoSPECT CT data, for example.