Exporting regions of interest in Osirix

I became a Mac user a few years ago, so by far the best DICOM software for me is Osirix. 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. In addition, the help available on the Wiki and in the forums is limited and frustrating to search though. I did buy the book (Osirix: the pocket guide) which has some better explanations of the tools.

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. Here’s a step-by-step guide on how to go about doing it.

Open the series

To open selected series from multiple patients, start with the database screen. Holding the option key, click on the series under each patient that you want to open. Once they are all selected, press the 2D viewer key at the top of the window. Each series will open in a separate window. You can also just open one or a few at a time since series with many images can slow your computer down dramatically.

Create ROI’s

The ROI tools are located in the “mouse button function” area of the standard toolbar. It has many different options, from oval and square regions, to polygons and freehand pencil ROI’s. It’s worth trying them all out to see how they fit your needs. 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. To copy an ROI in the same series, you can use the dropdown ROI menu and choose “propagate 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. The selector tool is at the bottom of the ROI dropdown menu, and you’ll need it to activate any ROI.

Once you have your ROI in place, double click on it to open the ROI info panel. From here you can rename it, which will be useful once you have exported it to a spreadsheet. Single ROI’s can be exported directly from here as an .xml file. It has all the information, but you’ll have to cut and paste to extract it.

Open the ROI images in a series

The best way to export your ROI data is to use the ROI plugin. The ROI plugin comes with the latest version of Osirix, v.3.2. Unfortunately the export ROI plugin only works on ROI’s that are in the same series. So to make it work, you need to open the images with your ROI’s in a series together. First, close all the windows you have open by clicking on the database button. Your ROI’s will be saved automatically. Next, select the patients’ studies that you have created ROI’s in by using command/click. Then, right click with your mouse and select “open ROI images”. All of the images with ROI’s will open together in a single series.

Export the ROI data

Go to the plugin dropdown menu, and select export ROI. You do not need to select or activate the ROI’s before doing this. The plugin allows you to choose the filename and location for the file, and to choose between .xml and .csv. Click on .csv and save the file. Then from you spreadsheet program, choose file/import. Navigate to your .csv file and import the data. Most spreadsheets will recognize comma separated values and organize the data into columns for you.

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.