Trouble passing file locations to code

[shabedue]

Hi,

I'm having some difficulty passing the arguments (locations) to this code using the instructions. I am able to get the code to execute when I use ".\createDICOM.py Patient_folder_name input_folder output_folder" but the code doesn't find the files. Is this a valid way to pass these arguments?

Should patient_folder_name simply be the name of the folder in the Mount_0 directory? Should input_folder be the full file path and does it need to lead to the .tar folder?

Best regards, Max

[mogilnayr]

Hello,

I’m pretty much in the same situation as the person above and struggling with the supplying the arguments. My populated variables looks like this. Please advise, what am I doing wrong? I’m not clear on the input_folder setting. "This path points to the location of the tar file Mount_0 directory"

main(temppatientfolder, inputfolder, outputfolder) where temppatientfolder ="\SourcePinnacleTar\ZZZZ-LTBREAST-20041221144432-Fake,Name,-20-691.20041221144432\Institution_999\Mount_0\Patient_999" inputfolder = "C:\SourcePinnacleTar\ZZZZ-LTBREAST-20041221144432-Fake,Name,-20-691.20041221144432\Institution_999\Mount_0" outputfolder = "C:\TarToDicom\"

Thank You so much!

[shabedue]

Eh, I never managed to figure this out unfortunately. Let me know if you get it and good luck!

-Max

[mogilnayr]

I definitely will. I kind a must to figure this thing out, as I need to convert the Pinnacle to standard DICOM format. And unfortunately, I don’t find too many alternatives out there. Max, have you found any other way of converting?

Thanks, Ruslan

[shabedue]

I've heard there is a company that will do the conversion for you but that they're quite expensive. For now we're archiving everything in DICOM format going forward and extending support of our Pinnacle server.

[pchlap]

Hi @shabedue & @mogilnayr

A little while ago I migrated a lot of this code over to the pymedphys project. Some documentation on getting started with the Pinnacle Export Tool can be found here: https://docs.pymedphys.com/cli/ref/pinnacle.html

Overall the tool is still experimental. It is working quite well (at least for us) for CT, RTDOSE and RTSTRUCT. The RTPLAN might need some work.

Let me know how you go or if you need any advice in getting started.

Cheers Phil

[AndrewWAlexander]

Hi @shabedue & @mogilnayr

"patient_folder_ name" is the the name of the folder, whereas the other two input parameters are folder paths. You can think of the patient folder name as the ID number that Pinnacle used for that patient.

I had written an example of how to run the code in the wiki. If this is still unclear, please let me know.

Runscript

Execute ./createDICOM(patient_folder_name, input_folder, output_folder), where... patient_folder_name: is the folder within the Mount_0 directory that you want to convert to DICOM files. input_folder: This path points to the location of the tar file Mount_0 directory output_folder: This path points to the location of where the user wants to store the DICOM files on their platform