August 23, 2019

Cortical Reconstruction Process using FreeSurfer – Part 2

This workshop is the second part of a previous workshop , hence previous participants have priority to register.

Sydney Imaging brings together researchers and clinicians, through the provision of exceptional infrastructure and technical expertise, to tackle frontier questions in healthcare and medical research. One of the University of Sydney’s Core Research Facilities is Sydney Imaging located at the Charles Perkins Hub. These research precincts are dedicated to addressing major healthcare challenges – such as neurodegeneration, diabetes, obesity, cardiovascular disease, child development, mental health and ageing – and translating priority research discoveries into long-term clinical societal and economic benefits.

The University of Sydney is a partner of the CVL project and we are delighted to hold a training on how to use the CVL desktop for The University of Sydney staff and students using FreeSurfer as workflow example.

FreeSurfer is an open source software suite for processing and analysing human brain MRI images.


  • Basic concept understanding curvature, volumetry, cortical thickness. (Part 1)

  • Be able to visualise parcellations on structural scans using Freeview. (Part 1)

  • Be able to diagnose errors and have a few tips to troubleshoot those. (Part 2)

  • Be able to apply basic techniques for ROI editing. (Part 2)


General knowledge of human brain image analysis is assumed. Participants should be able to use basic command line examples.

For setting up accounts, participants will be asked to create an account in MASSIVE to use the CVL@MASSIVE a few days prior the workshop.


Thomas Shaw from the Centre for Advanced Imaging at The University of Queensland


The Characterisation Virtual Laboratory is a free cloud-based virtual desktop workbench to perform analysis of complex image and microscopy data. It serves to run analysis in a large computing infrastructure, all embedded in a web browser accessible using AAF (Australian Access Federation), and connected to a HPC (high performance computing) infrastructure. For more information please visit


About 800 different versions of tools for image analysis and visualisation are available through the CVL. A Virtual Laboratory, such as the CVL can save researchers time as they do not have to create and maintain their own online environments and tools.


Currently the virtual desktop service is provided by MASSIVE (Multi-Modal Australian Sciences Imaging and Visualisation Environment). To get started with the CVL at MASSIVE please follow the instructions here.

Contact for General enquiries about the CVL@MASSIVE

Email: MASSIVE helpdesk


Please register here.