STIR at the IEEE MIC 2017 Short Course on Image Reconstruction

This page is for participants in the Short Course on Image Reconstruction at the IEEE MIC. It will be updated with extra information before the course.
Please refresh the page when you re-visit. (In some browsers, such as FireFox, a normal Page Refresh doesn't work. On windows, right-click on the page, select This Frame and Release Frame).
Check the bottom of page for list of updates.

During the course, we will have practical exercises using STIR. 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 will 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).

Please note that the STIR version that we will be using is more recent that the current 3.0. Therefore, please use the virtual machine. If you really want to do this all yourself, you will need to get STIR from github, install SWIG, Python, etc and compile STIR with Python support. You would then need to get the example scripts from github. Don't try this at short notice...

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 k dot thielemans at ucl dot ac dot uk.

Initial download and installation

1. Make sure you have enough free disk-space on your laptop (~10GB for installation).
2. Install VirtualBox. Please note that this will require administrator permissions.
   There is more information in the installation instructions of the Virtual Machine
3. You can download a Virtual Image from CCP PETMR (use release 0.9.2). This VM contains SIRF (the CCP PETMR software for both PET and MR image reconstruction) but also STIR. 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
          update_VM_to_full_STIR.sh
          sudo apt-get install ipython ipython-qtconsole python-zmq csh
        

   
   Warning: this file is ~1.7GB. (You can of course download to a USB stick to save space on your laptop).

Next steps

The files might need another update before the course (but with minimal download time). In particular, the exercises themselves will still change. Therefore, please check this web-page occasionally.

Update process: open the terminal and just type

  update_VM.sh

We recommend that you get yourself (somewhat) familiar with VirtualBox and Ubuntu and iPython. Links are provided in the HELP.htm and on the Desktop in your VM and 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.

Page update history

1. 9 Sep, 10.00 UTC: first version
2. 16 Oct, 16.00 UTC: updated links
3. 20 Oct, 12:40 UTC: updated instructions for VM
4. 22 Oct, 14:15 UTC: updated link to README.md
5. 23 Oct, 9:00 EDT: updated list of Ubuntu packages to install

Contact webmaster.