This page contains information for participants of the Training School on the 5-6th of November 2019, right after the Synergistic Reconstruction Symposium. See http://synergimrecon.org/ for more information on the general arrangements.

The school will be centred around 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, and the Open Source Core Imaging Library (CIL) for CT reconstruction.

To be able to participate, students are asked to bring their own laptop if possible. We will not provide any computers, but you can of course sit with someone else.

Please follow the installation instructions below to get this on your laptop before the symposium. We will have a number of trainers available 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 school.

Please prepare for these exercises:

• Do initial reading (see bottom of this page)
• Download and install the VM
• Follow instructions to attempt to run 1 or 2 demos

Please note that the recent pre-release versions of SIRF version 2.1 and CIL version 19.10 are required for this school. These are preinstalled in the VM.

Virtual Machine installation instructions

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

Initial download and installation

Make sure you have enough free disk-space on your laptop (~10GB for installation).

Install VirtualBox 6.0.14. Please note that this will require administrator permissions.

Download the version 2.1 of the VM from this link.
Warning: this file is ~2.5GB. 

MD5SUM: ebb94f93335721ca34af34d5873e76df

Start the VM and log in with user sirfuser and password virtual

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).


./devel/CCPPETMR_VM/scripts/update_VM.sh
cd ~/devel/SIRF-Exercises/scripts/
./download_PET_data.sh
./download_MR_data.sh
cd ~/devel/CIL-Demos/scripts/
./download_data.sh


How to upload the data from the USB stick

If you got the data from a USB at the helpdesk, this command may help you upload the data to the VM.

scp -r -P 2222 path/to/data sirfuser@localhost:~/data
cd ~/devel/SIRF-Exercises/scripts/
./download_PET_data.sh
./download_MR_data.sh

Run the training material

The training material is pre-packed on the above mentioned VM. To be able to run the training on the VM:

1. Start the VM
2. Log in and open a terminal
3. For MR: start Gadgetron by typing gadgetron
4. start jupyter by opening a new terminal and typing jupyter notebook
5. On the host machine (the VM being the guest) open a browser and go to http://localhost:8888
6. the password for jupyter is virtual%1
7. Select the directory SIRF-Exercises for PETMR orientated examples
8. Select the directory CIL-Demos for XCT orientated examples

Background material

We will give brief introductions on PET, MR and CT before the exercises. If you are unfamiliar with PET and/or MR, you could benefit from checking out our more extensive PET and MR introductory lectures from a previous school at PSMR 2019.

We recommend that you get yourself (somewhat) familiarized 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 and the CIL Documentation.