![]() This crops the image data to the minimum axis-aligned bounding box of the labelled voxels. Surface3D: Image -> Crop Image Data to Labels (optional).Surface3D: Segmentation -> Select Thresholding Seed, then in any 2D view of the data click on any voxel of the object.Set the Lower Threshold to 1 and the Upper Threshold to the maximum possible value. Surface3D: In the Segmentation widget, click on the label to select it. ![]() Surface3D: Segmentation -> Add Object Label.Surface3D: Load the subject, select the object, and choose the appropriate DICOM stack from the list of Scan Data items.The individual object definitions should not have any image or surface files specified for them. xManager: Load the subject and add the DICOM stack as a Scan Data item for the session.Mimics: Export -> Images/Masks -> Images to DICOM.Mimics: Turn off Visibility for all masks except the object mask you just created.Choose the black color in the bottom left of the color options. ![]() Mimics: Right click on the mask and select Properties….Mimics: Rename the new mask to something appropriate for the object being segmented.Set Mask A to the All mask, the Operation to Minus, Mask B to the object mask, and Result to a new mask. Mimics: Select Boolean Operations from the Segment toolbar.Mimics: Create a mask covering the object of interest, using the various segmentation tools available.Mimics: Select the entire threshold region.Mimics: Select New Mask from the Segment toolbar.The steps for processing an object with this method are: In each DICOM stack, all voxels representing the object of interest have their original intensities (Hounsfield units for CT) and all other voxels are set to zero. In this case you must export from Mimics a DICOM stack for each object. 3D reconstruction is performed in Surface3D. Method 1: Segmentation is performed in Mimics. For ease of description this guide will assume you are using Mimics and MeshLab, but any of the other programs could be substituted for those. The best one for you depends on your data set and your level of expertise with the other programs. There are two primary methods of integrating data from these third-party programs into DSX Suite. Before continuing, please familiarize yourself with the DSX terminology for Image and Surface Files. This guideline is designed to help you integrate the outputs of those programs into DSX Suite. Nevertheless, if you already use one or more of these third-party programs for segmentation or 3D reconstruction, we encourage you to continue using them. The primary benefit of Surface3D is that it is integrated into the DSX Suite so that updating the subject file and handling reference frames and file formats consistently is automatic. It is to provide a solution to users who do not currently use these other prorgams and whose segmentation and surface smoothing needs are relatively simple. Our goal with Surface3D is not to replace these programs, which are robust, well-maintained, and widely used. Additionally, there are open-source programs with powerful tools for manipulating surface models, such as MeshLab and Blender. These programs provide sophisticated segmentation functions as well as tools for decimating and smoothing the polyhedral surface models. ![]() There are many third-party software packages for segmenting 3D image data (segmentation) and creating surface models (3D reconstruction), including Mimics, ScanIP, and 3D Slicer.
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