18.1 Loading 3D image data

FEBio Studio has several capabilities for rendering and overlaying 3D image data. In order to visualize a 3D image, you must first load a 3D image stack into the active model. Then, you need to attach one of the 3D image rendering tools to the image stack.

FEBio Studio uses SimpleITK to read and manipulate image data, and so it supports reading a large number of image formats. At the moment, FEBio Studio does only supports single channel, 8-bit images. When a higher bit image is loaded in, it is scaled down to 8 bits. Multichannel images (including color images) cannot be read in at all. To load image data, select the File → Import Image from the main menu, and then select the type of image that you would like to import, which will show the standard File Open dialog box. Locate the image file on the file system and click OK.

By default, the image data will be loaded into the active model. Thus, if you wish to view the image on top of a FE model, you first need to load that model, make sure it is active one, and then load the image data. When the image data is loaded in, a 3D volume renderer will be added to your model, displaying the image.

Supported Image Types

Raw Raw images contain no header information, and so in order to import them, you must provide information about the physical location of the image, and the physical and pixel dimensions of the image. When you import a raw image, a dialog box will appear where you can enter this information.

DICOM DICOM images are read using SimpleITK. In order to load in a sequence of DICOM images, simply select one of the DICOM files from the File Dialog. FEBio Studio uses builtin SimpleITK functionality to parse the header data of the DICOM images to locate and read all of the files that belong to the same dataset as the file you specified.

TIFF TIFF images are read using SimpleITK. To load in a TIFF image, simple select it from the File Dialog.

OME TIFF OME TIFF images are read using SimpleITK. To load in an OME TIFF image, you should select the xml file containing the OME header data from the File Dialog.

Image Sequence If you have a sequence of 2D image files that together make up a single 3D image, you can load them in using this option. Simply select all of the images files that correspond to your image stack in the File Dialog. To ensure that they are loaded in the proper order, please make sure that they are organized alphabetically by file name. Do not use this option to load in a sequence of DICOM files. Use the DICOM option instead.