MRM Highlights
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By Mathieu Boudreau
This MRM Reproducible Research Insights interview is with Ayse Sila Dokumaci, a researcher at King’s College London. Her paper entitled “Simultaneous Optimization of MP2RAGE T1-weighted (UNI) and FLuid And White matter Suppression (FLAWS) brain images at 7T using Extended Phase Graph (EPG) Simulations” was chosen as this month’s Highlights pick because she shared code that reproduces the authors’ simulations which was done using another open-source software package (EPG-X).
To learn more, check out our recent MRM Highlights Q&A interview with Ayse Sila Dokumaci and David Carmichael.
General questions
1. Why did you choose to share your code/data?
We were encouraged by MRM’s open research policy. I was hesitant at the beginning because the code is far from perfect, but it was good enough to lead to the data presented in the paper so hopefully it will be useful for other researchers too.
2. What is your lab or institutional policy on sharing research code and data?
The institutional policy is to share code used in research by default. Sharing data is generally preferred and encouraged although with patient data there are sometimes restrictions.
3. At what stage did you decide to share your code/data? Is there anything you wish you had known or done sooner?
This was decided during the writing of the manuscript. I commented my code from the beginning of the development stage, and this proved to be a great help when preparing it for publication.
4. How do you think we might encourage researchers in the MRI community to contribute more open-source content along with their research papers?
We see the value of open-source content because there is a huge investment of time for software development – the more it is used, the better and the more quickly we can get to the important questions rather than coding from scratch. It is also critical for reproducibility. However, it is not valued the same way as papers and grants, and you do not get more credit for it. In addition, it is an investment of time and energy to answer potential questions and maintain the content.
Questions about the specific reproducible research habit
1. What advice do you have for people who would like to get started with extended phase graph simulations?
The base code for EPG-X simulations is available from Dr. Shaihan Malik’s GitHub: https://github.com/mriphysics/EPG-X. A lot of information is available there, including examples and detailed descriptions of his implementations. I found Dr. Matthias Weigel’s review article “Extended phase graphs: Dephasing, RF pulses, and echoes – pure and simple” useful for learning more about EPG simulations in general. That paper provides some examples for MRI sequences, and a good way to start would be to replicate the examples shown in Dr. Weigel’s paper using Dr. Malik’s EPG codes. After doing that myself, I felt confident enough to check the details of Dr. Malik’s code and build on it.
2. Can you share tips or additional resources on how to use EPG-X?
I am sure there are many other resources, but three additional papers worth consulting would be the original EPG theory from 1991 by Professor Juergen Hennig, published in two parts (Hennig, Concepts Magn Reson 1991), and Dr. Malik’s EPG-X work (Malik et al., MRM 2017).
3. How do you recommend that people use the project repository you shared?
I put some effort into providing a ReadMe guide in the repository, so I hope that it will be helpful to get people started. Otherwise, they can contact me with any questions ?
4. Are there any other reproducible research habits that you didn’t use for this paper but might be interested in trying in the future?
I am paying more attention to what others are doing in terms of reproducible research.
