The original set of images, as well as subsequent iterations of these are available from. I will provide the steps used to create a three-dimensional reconstruction in Osirix from a user's images which were sent to me. Because of this, the three-dimensional reconstructions are based on the grayscale representation of any color images used as input for the system. Typically, this data is grayscale rather than color. You also have to realize that Osirix was written primarily for radiographic data. If correct aspect ratios and calibration are not needed, suitable pixel sizes and spacing to produce a reasonable reconstruction can be used. The names of the images must sort in geometric order corresponding to the location of the image slice when they are sorted by name in the Finder.Ī method for determining the pixel size and spacing of the images must be available to get geometrically accurate reconstructions. The series of images needs to be placed in a separate directory for import. The cross-sections need to be spaced at uniform intervals through the three-dimensional volume.Įach of the cross sectional images needs to be aligned to the image below and above.Įach of the cross-sectional images needs to be the same width and height in pixels. The input image data needs to have the following characteristics: This process is actually quite easy to achieve, however, certain specifications for the input data needs to be observed. Users of Osirix have asked on multiple occasions how to produce three-dimensional reconstructions from a series of images which are two-dimensional slices through a three-dimensional structure. That’s it! Now you have a spreadsheet that includes the mean, minimum and maximum values of your ROI, number of pixels, and standard deviation.Stereotactic Radiosurgery Institute, Gurnee, IL Most spreadsheets will recognize comma separated values and organize the data into columns for you. Then from you spreadsheet program, choose file/import. The plugin allows you to choose the filename and location for the file, and to choose between. You do not need to select or activate the ROI’s before doing this. Go to the plugin dropdown menu, and select export ROI. All of the images with ROI’s will open together in a single series. Then, right click with your mouse and select “open ROI images”. Next, select the patients’ studies that you have created ROI’s in by using command/click. First, close all the windows you have open by clicking on the database button. So to make it work, you need to open the images with your ROI’s in a series together. Unfortunately the export ROI plugin only works on ROI’s that are in the same series. The ROI plugin comes with the latest version of Osirix, v.3.2. The best way to export your ROI data is to use the ROI plugin. It has all the information, but you’ll have to cut and paste to extract it. Single ROI’s can be exported directly from here as an. From here you can rename it, which will be useful once you have exported it to a spreadsheet. Once you have your ROI in place, double click on it to open the ROI info panel. The selector tool is at the bottom of the ROI dropdown menu, and you’ll need it to activate any ROI. To copy it to a different patient or series, use command/C when the ROI is selected, then command/V on the image you’d like to place it on. To copy an ROI in the same series, you can use the dropdown ROI menu and choose “propagate ROI”. The repulsor tool (yellow circle) allows you to change the shape of several of these ROI’s, or you can click on the drag points to change the outline. It’s worth trying them all out to see how they fit your needs. It has many different options, from oval and square regions, to polygons and freehand pencil ROI’s. The ROI tools are located in the “mouse button function” area of the standard toolbar. You can also just open one or a few at a time since series with many images can slow your computer down dramatically. Each series will open in a separate window. Once they are all selected, press the 2D viewer key at the top of the window. Holding the option key, click on the series under each patient that you want to open. To open selected series from multiple patients, start with the database screen. Here’s a step-by-step guide on how to go about doing it. My goal was to be able to create ROI’s on CT images of several patients, and export them into a spreadsheet format for a research project. I did buy the book ( Osirix: the pocket guide) which has some better explanations of the tools. In addition, the help available on the Wiki and in the forums is limited and frustrating to search though. The open source, free software has lots of great features, but for users of eFilm (and former PC users) the interface is not always obvious. I became a Mac user a few years ago, so by far the best DICOM software for me is Osirix.
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