OsiriX

What is Osirix?

OsiriX

OsiriX is a medical imaging program developed by Dr. Osman Ratib (UCLA) and Dr. Antoine Rosset (University of Geneva) in order to display and analyze large radiological data sets on a desktop computer. OsiriX, like 3D Slicer, is built on the ITK and VTK programming toolkits and takes advantage of Mac OS X specific graphical and computing capabilities.

OsiriX is able to generate isosurface models and volume rendered models from data cubes. OsiriX allows the user in real time to change the displayed intensity level, crop the models without losing the data, manipulate the model and viewing angle, and use a variety of projections (e.g. maximum intensity projection). The displayed data can be output as an image, a QuickTime movie, or a QuickTime VR object (see the movies page for more examples). OsiriX’s real-time modeling and rendering capabilities make it a strong tool for data exploration.

For more information, check out the OsiriX Website.

Viewing Astronomy Data in OsiriX

Unfortunately, the current version of OsiriX does not support the FITS or NRRD file formats. Instead, if viewing astronomy data, a user needs to convert their FITS file to one of the supported medical formats (e.g. DICOM, ANZ), or print out the FITS cube as a series of images in a supported format (e.g. TIFF, JPG, etc.) which can then be imported into OsiriX.

If you would like to read your data into OsiriX as an analyze (ANZ) file, you can use fits2itk, but instead of adding a ".nrrd" extension to the output file, add ".hdr". (You will also need to add assign a non-zero number to all NaN pixels by adding "-N _number_" to your command line since OsiriX will sometimes crash due to NaN pixels.) This will output an ANZ file in the form of an image (.img) and header (.hdr) file. To read this into OsiriX, follow the instructions below and at 3. select both the .img and .hdr files. Please be aware that OsiriX is unable to preserve axis orientation. The only way at the moment to preserve the FITS cube's orientation is to read it into OsiriX as a series of image files.

AstroMed plans to integrate a better solution into its future versions of fits2itk. In the mean time, feel free to try OsiriX with the sample data below.

Sample Data and Download instructions

Note: OsiriX is a Mac only application. The AstroMed development team is working to incorporate volume rendering capabilities into future version of 3D Slicer which will operate on all platforms.

To set-up and download OsiriX, follow the instructions at: http://www.osirix-viewer.com/Downloads.html

Perseus

To view the COMPLETE Survey's 13CO data of the Perseus star-forming region in OsiriX, follow the instructions below:

  1. Download the sample data, and unzip the directory.

  2. Open the OsiriX application.
  3. Click the "Import" button, select all the TIFF images in the sample data directory, and click "Open".
  4. Double-click on the "patient's name" (i.e. "thirteenCO_001.tif"), or the image in the lower right, to open the "2D Viewing mode".
  5. Moving the slider along the top of the image will go through the data slices. To adjust the brightness/contrast, click on the image and move the mouse left/right or up/down.
  6. To view the data in 3D, click on the "2D/3D" button, and select "3D Volume Rendering".
  7. To display the data correctly, enter "1" into the following fields of the pop-up window: "Pixel X resolution", "Pixel Y resolution", and "Slice interval".
  8. To orient the data to the "RA-DEC" view, select "axial view" from the "3D Viewer" menu on the toolbar. Click on the image and rotate freely with the mouse. To adjust the brightness/contrast, use the gradient-button in the upper left corner. To zoom in-and-out, click the magnifying-glass-button in the upper left and move the mouse up-and-down over the image.

Contact

If you would like to receive updates on the project and notifications of new downloads, please send an email with "subscribe" in the subject header to our announcement list, iic-astromed-announce@harvard.edu.

If you have any questions about the project or using OsiriX with our sample data sets, please send an email to iic-astromed-info@harvard.edu.

Also, feel free to refer to our contact page.

OsiriX (last edited 2011-02-18 17:31:29 by borkin)