"List Index Out of Range" Error with CatPhan504 Analysis

[anaiska27]

Hello GitHub Community,

I hope this message finds you well. I am reaching out for assistance as I've encountered an issue while analyzing my CBCT images using Pylinac's CatPhan504 module.

Upon attempting to analyze my CBCT data, I consistently encounter the error message "list index out of range". Unfortunately, I'm unsure about the cause of this error and how to resolve it.

I suspect that the error may be related to the configuration of my CatPhan504 phantom. It's possible that my phantom setup differs from the standard configuration outlined in the Pylinac documentation.

Here's the code snippet I'm using for the analysis:
from pylinac import CatPhan504
from tkinter import filedialog

cbct_folder = filedialog.askdirectory()

mycbct = CatPhan504(cbct_folder)
mycbct.analyze()
print(mycbct.results)

I would greatly appreciate any insights or guidance on how to troubleshoot and resolve this issue. If anyone has experienced a similar problem or has expertise with Pylinac's CatPhan504 module, your help would be invaluable.

Thank you in advance for your time and assistance.

[jrkerns]

Can you attach your scan?

[anaiska27]

Yes, here it is
18112021.zip

[crcrewso]

I'm concerned about the image quality of the dataset, the first two images are adjacent slices, showing a high variance in signal to noise slice to slice. I can't even discern all of the HU regions for a 504 phantom. The third shows significant artifacts. Is it possible the dose rate used was too low?

[anaiska27]

It is a CBCT. And I made 2 protocols : head and pelvis. I didn't try with the 2 protocols but I think I will have the same problem

[crcrewso]

I think I see the problem, there's no empty slice at the end of the phantom.

[jrkerns]

Newer versions of pylinac give a better error message. It looks like the scan is just one slice short of being considered complete. It would be best if you could move your phantom to be more centered about the CTP404 (HU linearity) module. This can also be solved by overriding the module locations but the former is preferred.

[anaiska27]

Thanl you a lot
Can you just explain me how to fond the module's offsets please ?

[anaiska27]

I tried to add a slice at the end but I have the same error message...
I also tried to change the module locations but same error ...

[crcrewso]

So the slice you added to the end wasn't of air but was the same image as slice 93?

[anaiska27]

Yes, I had a 88 slices scan so I added a slice n° 89, which was a copy of the slice n°88

[crcrewso]

I can see the confusion, sorry, for the algorithm to properly detect the phantom orientation there needs to be an air slice at one end of the dataset.

[anaiska27]

Oh okay, so I need to do the same but with an air slice at the end ?

[anaiska27]

I see that in my scan, there no air slice ...

[anaiska27]

18112021.zip
Last try : I added an air slice at the beginning and at the and of the phantom but I still have the same error...

[crcrewso]

Is this phantom a Catphan504 or a Catphan500? The reason I ask is because the modules appear to be in a non-standard order for a Catphan504, and the HU module looks more like the CTP401 than the CTP404

[anaiska27]

I asked the physicists and they told me that it is a 504 but I agree with you that the module seems to be a 401...