My name is Nevin, I am a M.Sc Medical Physics student at the University of Canterbury, New Zealand. I am currently using Pymedphys, specifically the Gamma function to calculate the gamma from DICOM images. However, I have some questions I was hoping you could answer.
Firstly, from the “Gamma from DICOM” How-to guide (Gamma from DICOM — PyMedPhys). I noticed that when using the provided logfiles, there were several gamma evaluation/reference, dose difference and local gamma images generated. I was a bit confused about this as when I did the same for my DICOM images, I only got one set of gamma evaluation/reference, dose difference and local gamma images generated. I was wondering what the difference is between the various sets of images?
Secondly, I was hoping you could explain what the set of images with the gamma evaluation/reference, dose difference and local gamma images meant? I have been able to generate the images using the provided code but both me and my supervisor are unsure as to what the images specifically mean. For example, in this image
Does the blue coloured part of the Local Gamma image show where the gamma analysis fails for the evaluation against the reference image? If so, why does the dose difference not align with this particular image?
For reference, I have also attached the particular images I am using for my project, these are TOPAS generated DICOM images.
Thanks for posting this within the PyMedPhys community forums .
At first glance I notice that you have very small numbers in use:
Would you be able to start by finding the slice where you have the most dose, plotting the evaluation and reference for that slice and see if it makes sense?
There’s a bit going on in your post, before addressing the other points it’d be helpful to get on top of what data we’re working with.
Also, the following how-to guide shows the calculation of gamma from a bit more first principles:
Once you have a slice pulled from your eval dataset, and a slice pulled from your reference dataset would you be able to run gamma over them in a way similar to that second tutorial?
Also, here is the raw Gamma API reference, which might be helpful:
The reference and evaluation images I posted were taken by following the second tutorial, from reading the code I assumed it was taking the highest dose slice from the evaluation and reference datasets. I am not sure as to how to take the highest dose slice from the reference and evaluation datasets and run gamma over them individually. Would you be able to help me with this?
Also, in regard to the type of data this is, this is a DICOM image generated in TOPAS from 100 histories on a 40x40x40 water phantom. The low dose may be due to the low number of histories taken for the evaluation and reference datasets.
Glad I’ve been able to help. Also, if you happen to come up with a Notebook that you think others starting out like yourself might benefit from being able to read, let me know, I’ll put it up on the website
I can definitely look into making a Notebook! Also, I was wondering why there are so many sets of graphs generated? Is each set to do with a specific depth of the phantom? Or is it the dose build up over time with the most recent one being the slice with the highest dose distribution?
Thank you for that, sorry to bother you again but I have another question. Looking at the code and the image from the “Calculate and Display Gamma” section from “Gamma from DICOM” I noticed that the image below had no labels on the x or y axis. I assumed that the x axis was gamma and the y axis was pixels but I am not sure if the y axis are pixels. I was also a bit confused because the title suggests the DD and DTA are 0.5% and 0.5mm but the input values are 1% and 1 mm.
Could you please clarify this?
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