Error when computing dose [Not Found Error]

General
1

Dear Developers,

Thanks for providing the powerful OpenTPS tool. I have problems when computing the MC2 dose. I have attached the screenshot of the terminal for your reference. Seems that the three ‘not found’ cause the issue but I cannot locate the ‘not found‘ warning. Thanks in advance for your help.

Ronald

螢幕截圖 2025-10-24 下午4.56.58
螢幕截圖 2025-10-24 下午4.56.581640×1176 471 KB

2

Hi All,

I finally figured out the issue! The ‘Not Found’ message and the syntax error are all caused by the CRLF (carriage return) of the Windows system when clicking “Enter”. As the figure ‘Before Modification‘ shows, ‘^M’ appears at the end of each line, which indicates CRLF. However, the Unix system requires LF at the end of each line. Here I provide my solution for you who also uses the Unix system, and I believe it will save lots of time.

  1. Go to the directory where the MCsquare shell script is saved (NOT the OpenTPS_workspace as it will be re-created every time we calculate the dose)
  2. Open the terminal under the desired directory
  3. Use the command: ‘dos2unix MCsquare’

You may also meet the “permission denied“ issue when executing the mcsquare program. Suppose the shell script will call the MCsquare_linux_avx512, then just add ‘chmod +x MCsquare_linux_avx512‘ command before calling the MCsquare_linux_avx512 program in the shell script.

Before Modification
Before Modification1346×497 78.9 KB

Best,

Ronald

3

Dear Ronald,

Indeed, this is a common bug in OpenTPS. Would you mind sharing how you installed the package so that we can prevent this from happening again?

I recognize a Ubuntu terminal, are you remoting into it, or is it your main OS? Because this issue can also occur if you’re using an interpreter over SSH with PyCharm (it basically works like an rsync).

Best regards,
Eliot

4

Dear Eliot,

I tried both the conda installation (easy quickstart) and the git-clone installation (advanced quickstart), and the issue existed in both installations. Yes, my main OS is Ubuntu.

By the way, I used REGGUI before for mc2 calculation workflow, and it provided the material overridden function and the forcing material function. In the OpenTPS GUI, I can only see the ‘Overwrirte outsie this ROI‘ option. As material overriden is quite common in our center (override implant, couch, and so on), may I ask if this function will be provided explicitly in the future?

Best,

Ronald

5

Hello,

Bug is fixed in the merge request 234, that will be available as soon as the new release of OpenTPS is out.

Regarding the feature you ask, I will be sure to bring that up to our next internal meeting and confer with the rest of the development team how to try to bring this feature.

Best,
Eliot

6

Hi Eliot,

Thanks so much.

I will also try to implement the features on my side.

Best,

Ronald

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