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Creating 4D Images

You can create a time-enabled 4D dataset from multiple volumetric datasets in the Create 4D Image dialog, shown below.

Create 4D Image dialog

A. List of images B. Output parameters C. Output options

The top section (A) of the Create 4D Image dialog contains a list of all the datasets that you selected for creating a single 4D dataset, while the bottom section (B and C) contains the selectable settings and export options. You can export 4D datasets in the TIFF file format directly from the Create 4D Image dialog, or you can choose to create and add the 4D dataset to the Data Properties and Settings panel.

All of the datasets you select for creating a 4D dataset must be of the same data type. If required, you can restructure your image data (see Converting Image Data). For best results, the orientation of all datasets must be consistent. If required, you can invert the axes of a dataset (see Inverting Datasets). In addition, all datasets should be accurately registered (see Registering Datasets).

Settings and Output Options

The following settings are available for creating 4D datasets.

Settings
	Description
Show visual box	If selected, the reference box that determines the dimensions of the output 4D dataset will appear in the current scene views. The initial size and orientation of the reference box is modeled on the selected datasets to provide the best initial fit.
Out-of-bounds value	Lets you assign a data value to voxels that are out-of-bounds. Out-of-bounds voxels are voxels that are included in the box shape, but do not intersect with any of the voxels of the datasets selected for creating the 4D dataset.
Resolution	Lets you choose the resolution of the output 4D dataset as follows: Most precise… Uses the smallest voxel size of all datasets selected for the operation. User defined voxel size… Lets you choose the required values for spacing in the X, Y, and Z axes, which determines the voxel size. You should note that increasing spacing along an axis will reduce the number of pixels along that axis by downsampling. Conversely, decreasing the spacing along an axis will increase the number of pixels along that axis by upsampling. Note User-defined voxel size selections are limited to a factor of 10 of the original image data. User defined matrix… Lets you choose the matrix of the output dataset as the number of pixels in the X, Y, and Z axes. You should note that increasing the number of pixels along an axis will decrease the corresponding spacing value, while decreasing the number of pixels along an axis will increase the corresponding spacing value. NOTE In all cases in which the resolution of the original image data is changed, the geometry defined by the referenced box — which is calculated as the [(number of pixels)*spacing] — will be maintained. Interpolation will be applied, as required.

The following output options are available for exporting and creating 4D datasets.

Output options
	Description
Dataset size	Indicates the file size of the 4D dataset that will be exported or created.
Dataset name	Lets you enter a name for the 4D dataset that will be exported or created.
Export	Lets you export the 4D dataset in the TIFF file format directly from the Create 4D Dataset dialog.
Create	Adds the newly created 4D dataset to the Data Properties and Settings panel.

How to Create a 4D Image

Load all of the datasets that you plan to include in your 4D dataset (see Multi-Image Visualizations).
For best results, make sure that the orientation of all the datasets you include is consistent. If required, you can invert the axes of a dataset (see Inverting Datasets).
In addition, all of the datasets you select for creating a 4D dataset must be of the same data type. If required, you can restructure your image data (see Converting Image Data).
If required, adjust the position of one or more of the datasets so that all of the important features are aligned.
You can use the tools on the Move panel to manually position a dataset (see Translating and Rotating Objects) or you can automatically register datasets with Dragonfly's feature-based registration workflows (see Registering Datasets Automatically). You can also align the centroid of a selected dataset with another object by choosing the pop-up menu item Align Centroid With.
Select all of the datasets you plan to include in the 4D dataset in Data Properties and Settings panel, recommended.
The initial size and orientation of the reference box will be modeled on the selected datasets to provide the best initial fit.
Right-click and then choose Create 4D Image in the pop-up menu.
The Create 4D Image dialog appears.
Make the reference box visible by checking the Show visual box item, recommended.
Adjust the size and/or position of the reference box, if required. The dimensions of the referenced box will determine the dimensions of the output 4D dataset.
You can edit the size of the box and its position in any 2D view or in the 3D view by simply dragging the available control points (see Editing Shapes).
Drag other datasets you want to include in the 4D dataset from the Data Properties and Settings panel to the Create 4D Dataset dialog, if required.
You can also remove a selected dataset by clicking the Remove Dataset button.
Choose the settings that you want to apply to the output dataset, as described in Settings and Output Options.
Out-of-bounds-value… If required, select the data value that will be assigned to voxels that do not intersect with the datasets selected for the 4D dataset, but that are included within the reference box.
Resolution… Choose a resolution — Most precise, User defined voxel size, or User defined matrix — as required. You should note that the estimated memory size will be updated automatically if you increase or decrease the resolution of the output dataset.
Enter a new name for the output file in the Dataset name edit box, if required.
Do one of the following:
- Click the Export button to export the 4D dataset to a local or network drive or to a portable storage device. Datasets exported directly from the Create 4D Dataset dialog are saved in the TIFF file format.
- Click the Create button to add the 4D dataset to the Data Properties and Settings panel.
  See Exporting 4D Images for information about exporting 4D datasets from the Data Properties and Settings panel.

Exporting 4D Images

You can export 4D images from the Data Properties and Settings to a number of different file formats, including *.ORSObject, *.raw, *.tiff, and *.hdr.

Export options
	Description
ORS (*.ORSObject)	ORS Object files are proprietary binary formatted files in which data is written sequentially and XML (Extensible Markup Language) is appended after the binary data.
Raw (*.raw)	A basic file format that saves images or stacks as raw pixel data without a header. Suitable for transferring files between applications and computer platforms. When saving RAW files in Dragonfly, header information is saved in an accompanying DAT file. If you choose .raw as the file format for your 4D data, you can select the Output all images into one file* option as shown below.
TIFF (*.tif)	A widely supported lossless compression file format for storing bit-mapped images, TIFF files can be any resolution, as well as uncompressed or LZW compressed. The following options are available when saving data in the TIFF file format. Use LZW compression… If selected, the TIFF file or files will be compressed using LZW compression, a lossless data-compression technique for reducing a file's size created by Abraham Lempel, Jacob Ziv, and Terry Welch. Output all images into one file… This file format differs from an image stack in that the entire volume is stored in a single file. Although the majority of TIFFs contain just a single image stored in a directory, some applications can generate multi-directory TIFFs that contain multiple images. Note The number of time steps in the data are not be encoded in TIFF files. You will need to enter the number of time steps in the Import Datasets, shown below, if you load the data back into Dragonfly.
Analyze 7.5 (*.hdr)	The Analyze file format was developed at the Mayo Clinic as part of a software package of the same name. Datasets in this format consist of small HDR files that describe the data and IMG files with the raw data. Although there are multiple versions of this format, Dragonfly only supports the 7.5 variant.