In this page we would like to introduce Mr. Jeremy Lee Hughes, one of our MSc graduates in Medical Physics.

Jeremy was a brilliant student and he has been accepted to enter the Radiation Oncology TEAP program at Peter MacCallum Cancer Centre, which is a leading oncology research institute, and professional oncologist training centre for cancer treatment, located in Melbourne, Victoria.

The title of his Masters project was: “Automated Analysis of Varian Log Files for Advanced Radiotherapy Treatment Verification: A Multicenter Study”.

His research was carried out under supervision of Assistant Professor Pejman Rowshanfarzad, Professor Martin Ebert, and Associate Professor Michael House.

Here are comments from Jeremy’s principal supervisor (Pejman):
“I found Jeremy highly intelligent and a quick learner. Jeremy has good analytical and programming skills. In his project on the analysis of dynalog files, he demonstrated a reasonable understanding of linacs and patient specific QA. During his project, he showed the ability to work independently with great creativity and enthusiasm. I outlined the scope of the work to be completed, and he successfully completed the tasks in time. He put in a lot of effort in his research and attended the office regularly not only during work hours but also many extra hours every week. His oral presentations in our weekly research meetings and discussion sessions were always impressive. He was friendly with everybody in the office making him a likable character.”


Jeremy kindly accepted to answer a few questions about his experience in our Medical Physics research Group.

Introduction and Current Role
My name is Jeremy Hughes. I completed my Masters of Medical Physics in 2015 and I am currently working part-time as a Scientific Officer at Genesis CancerCare in Bunbury, WA. Fairly soon, most likely by the time you are reading this, I will be starting a Medical Physics Registrar position in the wonderful state of Victoria where I will take up drinking coffee, wearing scarves, and working long hours into the night.

What did you enjoy most about UWA and Medical Physics research group?
The highlight of my time at UWA and the Medical Physics research group were the wonderful people and communities. The different clubs at the university, most notably the Postgraduate Student Association (PSA), helped me connect with different likeminded individuals as well as providing opportunities to present my work to my peers.

Can you give us your top three reasons to study Medical Physics?
1- It is a practical application of your physics degree with job prospects at the end. I will vouch for that even if it did take a year of constant rejections before I finally landed a job in Medical Physics. It was actually easier for me to get a job as an actor in a theatre troupe but that is by the by.
2- It is another 2 or so years you can put off joining the work force and continue living the university lifestyle.
3- Student Discounts. Oh and getting into a profession where you help others.

How do you feel you have made a difference in your field of research?
I don’t feel I have thus far. My Master’s work was fairly inconclusive from a clinical standpoint but it has placed me into a position where I will be able to make a difference.

What is your best advice to current students and Medical Physics applicants?
Is this what you want to do? Medical Physics is a practical application of physics. Equations are derived not from first principles but by tables of data and empirical evidence. It’s more Engineering than Physics which is not a bad thing, just a different thing.
The radiobiology aspect is fascinating but some other sections, the laws governing radiation safety, can be downright mind numbingly boring. But you should get used to that as a Medical Physicist because you are going to be working late into the night and on weekends. Those are the only times you will have access to the machines. As one Medical Physicist told me, “I hope you enjoy having lots of money but no time to spend it.”
Choose your thesis topic carefully; you’ll be working on it for the next 2 years so you best enjoy it.
Your supervisor is there to help. Ask them questions and listen to them. If they suggest you read something you better well read it because it will make your life so much easier down the track. You don’t want to be reading text books two days before your thesis is due. That is just a bad time.
Lastly make the most of your university lifestyle. Stay at the beach all day in the summer and then work on your project at night. Join clubs, pick up a hobby, start a one man comedy band and then realise you don’t actually know how to play one instrument let alone a whole band and then wonder what you are going to do with these 200 flyers that you printed out.
You’re flexible, set your own hours, but be sure to actually do work instead of browsing Facebook ad infinitum. Now stop procrastinating and get back to work.

Once again we congratulate Jeremy for his great achievements and wish him all the best for his future career as a Radiation Oncology Medical Physicist.

Here is the abstract of Jeremy’s thesis:
Varian linear accelerators store information of their deliveries in log files which can be extracted from the machine and analysed. These files contain a wealth of information, including the actual and expected position of each leaf throughout the treatment.
The analysis of Varian log files has been a growing field of interest ever since the turn of the millennia. The high resolution log files allow deep analysis into treatment plans delivered by Varian treatment machines.
This thesis undertook an international multicenter study that sought to find trends in the positional error of the MLC when compared to factors such as; the velocity of the leaves, the gantry angle, the age of the machine, the treatment site, the treatment modality, and the treatment machine. A program was devised in MATLAB to perform statistical analysis on the Varian log files. Additionally another MATLAB program was written to clinically assess these Varian log files.
By analysing the Varian log files, this thesis found a positive trend between the error of the MLC to the age of the machine. VMAT treatments had greater error than their dIMRT and Step and Shoot counterparts. The prostate treatment site had less error than the H&N and PPN treatment sites. And Varian Truebeam machines possessed less error, by a full order of magnitude, than Varian Clinac iX or Varian Trilogy machines. There was a trend towards greater error for leaves with increased velocity. In general there was greater error for leaves at positions more vulnerable to the force of gravity. This trend was not present for Sliding Gap tests delivered at discrete gantry angles.
Varian log files were used to assess thousands of deliveries performed by Varian linear accelerators. The information available in each file allowed trends to be drawn between the positional error of the MLC and the age, model, modality, treatment site, and leaf velocity.

And here is video recorded from one of Jeremy’s presentations at Sir Charles Gairdner Hospital about his research outcomes.

The code is available via this link. If you don’t have access to the Matlab software, there is a free access Python module called Pylinac you can look into (not developed by us).

Published paper using the Mountaingoat software: An Investigation of Multileaf Collimator Performance Dependence on Gantry Angle Using Machine Log Files

How to cite this article: 
Hughes JL, Ebert MA, McGarry CK, Agnew CE,Sabet M, Rowshanfarzad P. An investigation of multileaf collimatorperformance dependence on gantry angle using machine log files. J MedPhys 2021;46:300-7.
DOI: 10.4103/jmp.JMP_44_21


  • Andrea Flühs says:

    This is a very useful thesis; congratulations. I’m very interested in the program MountainGoat but the link to it in the thesis only shows the research home page. Is it possible to get it?
    Thank you very much.

    • uwamedicalphysics says:

      Hi Andrea,
      Have added a link to the post to access the code.
      Good luck

      • Ajaga Achidi says:

        Hello, I am currently working on a similar research topic similar to Jeremy’s. Is it possible I reach him for some technical assistance? mail or something please?

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