STIR at the IEEE MIC 2018 Short Course on Image Reconstruction

This page is for participants in the Short Course on Image Reconstruction (SC9) 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, check this page with additional links

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 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 15 minutes before the course to help with installation problems and will have some USB sticks with us as well).

We will also attempt to use 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 the STIR version that we will be using is much more recent than the current official 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.

We are using a VM based on a framework developed by the CCP PETMR project, but with tweaks for the STIR exercises.

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. We recommend to use VirtualBox 5.2.18, although different versions should work (but you might have trouble with the VirtualBox Guest Additions, see the installation instructions further on).
3. Download the STIR exercises Virtual Machine from here.
   Warning: this file is ~2GB. (You can of course download to a USB stick to save space on your laptop).
4. Install the VM, instructions are here (ignore links to the CCP PETMR download page and any mention of Gadgetron or SIRF)
5. Check-out the basic instructions on how to use the VM

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 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. 12 Oct, 07.00 UTC: first version
2. 7 Nov, 03:40 UTC: added links to the VM and instructions

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