CCP PET-MR

Collaborative Computational Project in Positron Emission Tomography
and Magnetic Resonance imaging

Training school on PET/MR reconstruction at PSMR 2019

After the success of previous years, there will be a (free) training school on PET/MR image reconstruction on Sunday 14th of April, organised by the CCP PET-MR team. The school will cover basic principles of the physics behind the acquisition process and image reconstruction methods used for both PET and MR (lectures' slides and videos can be found here). The school will include extensive practical sessions with the Open Source software Synergistic Image Reconstruction Framework (SIRF), which includes reconstruction methods for both PET and MR, and also image registration tools.

During the course, we will have practical exercises using SIRF, the Synergistic Image Reconstruction Framework which is open source . These exercises are an integral part of the course. To be able to participate, students are asked to bring their own laptop if possible.

We provide a Virtual Machine with everything preinstalled for the course. Please follow the installation instructions below to get this on your laptop before the conference. We will be available 30 minutes before the course to help with installation problems and will have some USB sticks with us as well. In addition, we will provide cloud-based access (thanks to Ben Thomas, UCL), but this will clearly depend on Internet access, so we strongly suggest to download the VM before the course.

Please note that SIRF version 2.0.0-rc1 is required for this school. Moreover, we have a dedicated repository with the exercises. Installing SIRF is not an easy task, therefore we suggest to use the virtual machine. If you really want to do this yourself, you will need to follow the installation instruction on our wiki. You would then need to get the example scripts from github

Please prepare for these exercises, see bottom of this page.

Virtual Machine installation instructions

If you have any problems, please first re-check this web-page. If you cannot solve your issue, please email Edoardo Pasca (edoardo.pasca@stfc.ac.uk).

Initial download and installation

  1. Make sure you have enough free disk-space on your laptop (~10GB for installation).
  2. Install VirtualBox 5.2.26. Please note that this will require administrator permissions.
    There is more information in the installation instructions of the Virtual Machine
  3. Download the version 2.0.0-rc1 (mirror) of the VM from the software framework page.
    Warning: this file is ~2.5GB
  4. After following the installation instructions of the Virtual Machine, please type the following in a terminal in the VM (note that this will take quite a while).

update_VM.sh

cd ~/devel/SIRF-Exercises/scripts/

./download_PET_data.sh

./download_MR_data.sh

 

Next steps

We recommend that you get yourself (somewhat) familiar with jupyter notebooks, iPython, VirtualBox and Ubuntu. Links are provided in the README.md. (this is a simple text file in Markdown format. It is nicely formatted on the web-site). It would also be useful to check some of the SIRF documentation.

More detail including the programme and registration information can be found at

https://www.psmr-conference.com/programme/petmr-training-school/

This also includes information specific to UK participants for help with travel costs (thanks to funding from the UK EPSRC). Please note that deadline for registration is 18th of March.

Page update history

  1. 8 Apr, 10.00 UTC: first version
  2. 9 Apr, 23:00 UTC, updated info
  3. 12 Apr 9:30 UTC, added download links

 

Tags: 
Excerpt: 
The school will cover basic principles of the physics behind the acquisition process and image reconstruction methods used for both PET and MR. The school will include extensive practical sessions with SIRF
News Date: 
Monday, March 18, 2019