Account creation and login

• Make sure that you are registered as a tutorial user. Your home page should look like this:


Launching simulations

You have access to 5 simulators:

1. FIELD-II for ultrasound imaging
2. SIMRI for MRI
3. Sindbad for Computed Tomography
4. PET-Sorteo for Positron Emission Tomography
5. GATE for radiotherapy
Choose 2 simulators and launch the test simulations.

Ultrasound

• Sample inputs are in /vip/Tutorial (group)/TestData/FIELD-II. Use the File Transfer in case you want to check or modify them (requires Matlab).
  More information about these parameters is available here.
• Launch and monitor the simulation as described here.
• Note that the simulation will compute a total of 17 radio-frequency lines. Each line is computed in a separate job. Merge and reconstruction are also computed in separate jobs.
• At the end of the simulation, outputs raw and img should contain this image (you can visualize it with VV):
  

MRI

• Sample inputs are in /vip/Tutorial (group)/TestData/Simri. Use the File Transfer in case you want to check or modify them.
  More information about these parameters is available here.
• Launch and monitor the simulation as described here. Note that you can simulate several image slices at the same time:
  
• At the end of the simulation, output outputFileLfn should contain an image looking like this (you can visualize it with VV):
  

Computed Tomography

• Sample inputs are in /vip/Tutorial (group)/TestData/Sindbad. Use the File Transfer in case you want to check or modify them.
  More information about these parameters is available here. The phantom used in this tutorial is XCAT. Due to licensing issues you cannot access it from the platform but you can use it to generate simulated images.
• Launch and monitor the simulation as described here. Note that the simulation will compute a total of 10 X-ray projections. Each projection is computed in a separate job.
  
• At the end of the simulation, output ResultFile should contain 10 tgz archives containing projection images looking like this. To visualize them with ImageJ, import 0deg0mm_img0_0.sdt as raw data, choose Width=672, Height=512, White is zero, Little-Endian Byte Order:
  

Positron Emission Tomography

• Sample inputs are in /vip/Tutorial (group)/TestData/Sorteo. Use the File Transfer in case you want to check or modify them.
  More information about these parameters is available here.
• Launch and monitor the simulation as described here. Note that the simulation will be split in 13 jobs.
  
• At the end of the simulation, a sinogram is available in output Sinogram. You can visualize it using Amide.

Radiotherapy

• Download and unpack the test simulation.
• Open mac/main.mac using GateLab. Launch, monitor and retrieve the simulation results as explained here.