3D Slicer



3D Slicer

Please check out the Slicer Web Page at http://www.slicer.org

The 3D Slicer is a software tool for guiding biopsies and craniotomies in the operating room, offering diagnostic visualization and surgical planning in the clinic, and facilitating research into brain shift and volumetric studies in the lab.

The 3D Slicer uniquely integrates several facets of image-guided medicine into a single environment. It provides capabilities for automatic registration (aligning data sets), semi-automatic segmentation (extracting structures such as vessels and tumors from the data), generation of 3D surface models (for viewing the segmented structures), 3D visualization, and quantitative analysis (measuring distances, angles, surface areas, and volumes) of various medical scans.

fMRI The image to the left was created by segmenting an anatomical MR scan to form 3D surface models of the skin and tumor (green). Functional MR data was segmented to build models of the motor cortex (yellow), auditory verb generation (red), and visual verb generation (blue). All these surface models are integrated in a 3D view along with 3 slices through the MR images. The slices are also shown in 2D views at the bottom. Note that the functional data is overlaid in color on the anatomical data.

We integrated the 3D Slicer with an open MR scanner to augment intra-operative imaging with a full array of pre-operative data. The same analysis previously reserved for pre-operative data can now be applied to exploring the anatomical changes as the surgery progresses. Surgical instruments are tracked and used to drive the location of reformatted slices. Real-time scans are visualized as slices in the same 3D view along with the pre-operative slices and surface models. The system has been applied in over 20 neurosurgical cases at Brigham and Women's Hospital, and continues to be routinely used for 1-2 cases per week.

The surgeon stands witin the gap of the interventional MR magnet (Signa SP - GE Medical Systems) The surgeon observes the display output of the 3D-Slicer on the overhead LCD monitor.

How to use the 3D Slicer

Get the Software

The 3D Slicer is freely available for research purposes. To obtain a copy, you need to read and agree with the 3D Slicer Software Licence Agreement, which explains that this software is made available for scientific research purposes only, and then complete the following form. If you indicate you agree with the 3D Slicer Software Licence Agreement, we will send you an email explaining how to access the software.

The capabilities for automatic registration, segmentation and integration with intra-operative imaging are not included in the current public release.


The software is currently available for the following platforms:

  • Sun UltraSPARC workstations running operating system Solaris 2.8 (also known as Solaris 8 or SunOS 5.8) and OpenGL 1.2
  • PCs running Windows2000 or WindowsXP
  • Since we give out all source code, users can compile it for other platforms such as Red Hat Linux 7.3 and SGI.


D. Gering, A. Nabavi, R. Kikinis, W. Eric L. Grimson, N. Hata, P. Everett, F. Jolesz, W. Wells III. An Integrated Visualization System for Surgical Planning and Guidance using Image Fusion and Interventional Imaging. In Proceeding of Medical Image Computing and Computer-Assisted Intervention (MICCAI), Cambridge England, Sept 1999. pp.809-819.
D. Gering. A System for Surgical Planning and Guidance using Image Fusion and Interventional MR. MIT Master's Thesis, 1999.
9.8M 22M
Surgical Planning Laboratory, Department of Radiology, Brigham and Women's Hospital