Brown 2015

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3D Slicer is an open-source software platform for medical image analysis and 3D visualization used in clinical research worldwide. The software is supported by a multi-institution effort of several NIH-funded consortia, which include the Neuroimage Analysis Center (NAC), the National Center for Image-Guided Therapy (NCIGT), and the Quantitative Image Informatics for Cancer Research (QIICR). Funding from several other countries contributes to some aspects of the software. 3D Slicer provides clinical researchers easy access to advanced image analysis tools that can be run on their Windows, Mac or Linux laptop computer with their own data. The software is distributed under a BSD-style free open source license with no restriction on use. 3D Slicer is not FDA approved or CE marked, and is for research use only. The platform integrates functionalities for image display, image analysis and quantitative imaging, as well as other utilities which include tool tracking and real-time data fusion for image-guided therapy.

The 3D Slicer Brown workshop is a full day course that will combine a series of lectures and hands-on sessions using the 3D Slicer software. The morning session will provide an introduction to the basics of data loading, 3D visualization and image registration. The afternoon session will focus on fundamental and practical aspects of Diffusion MRI analysis.

Workshop Organizers

Tentative Agenda

  • 10:00-10:15 am Computer setup assistance by the instructors
  • 10:15-10:30 am Welcome and Goals of the Workshop (Derek Merck)
  • 10:30-11:00 am Introduction to the 3D Slicer software and community (Sonia Pujol)
  • 11:00-12:00 pm Hands-on session 1: 3D Data Loading and Visualization (Sonia Pujol)
  • 12:00-1:30 pm Lunch Break
  • 1:30 pm-3:00 pm Hands-on session 2: An Introduction to Diffusion Tensor Imaging (Sonia Pujol)
  • 3:00 pm -3:15 pm Coffee Break
  • 3:15-4:15 pm Hands-on session 3: White Matter exploration for Neurosurgical Planning (Sonia Pujol)
  • 4:15-4:45 pm DTI tractography: Validation Aspects (Sonia Pujol)
  • 4:45-5:00 pm Questions from the audience and concluding remarks


  • Date: November 19, 2015
  • Location: Brown Digital scholarship lab (DSL), located at the Rockefeller library on Brown campus.
  • Pre-requisite: There is no pre-requisite per se, but a basic knowledge of medical imaging is recommended.
  • Fee: This workshop is free
  • Workshop Materials: The workshop will be a series of hands-on sessions using Slicer 4.5 release versions (

Participants need to bring to the workshop a laptop with at least 2 GB of RAM (the more the better), and dowload the following datasets