CCP SyneRBI

Collaborative Computational Project in Synergistic Reconstruction for Biomedical Imaging

Training school on PET/MR reconstruction at PSMR 2018

This page was for participants in the Training School at PSMR 2018.

Check here for the recordings of the training session.

SIRF workshop at PSMR2018

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 hope to be able to provide the exercise via cloud computing, but cannot guarantee that yet.sirf

Please note that SIRF version 1.1.1 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 5.2.12. Please note that this will require administrator permissions.
    There is more information in the installation instructions of the Virtual Machine
  3. Download the version 1.1.1 of the VM from the software framework page.
  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

Warning: this file is ~1.7GB.

Next steps

We recommend that you get yourself (somewhat) familiar with VirtualBox and Ubuntu and iPython. Links are provided in the README.md. (this is a simple text file in Markdown format. It is nicely formatted on the web-site).
Here is some suggested material:

  1. If you have never used a Linux/Unix terminal before, have a look at this tutorial.
  2. The official Python tutorial. Just read Section 1, 3, a bit of 4 and a tiny bit of 6.
  3. Examples for matplotlib, the python module that allows you to make plots almost like in MATLAB.

It would also be useful to check some of the SIRF documentation.

Page update history

  1. 11 May, 10.00 UTC: first version
  2. 17 May, 20:20 UTC: updated version for release 1.1.1
  3. 18 May, 09:20 UTC: updated with download data script
  4. 21 May 10:00 UTC: added group photo